481 lines
16 KiB
Java
481 lines
16 KiB
Java
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package eu.dnetlib.dhp.oa.graph.dump.skgif;
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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.stream.Collectors;
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import javax.validation.constraints.AssertTrue;
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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.FilterFunction;
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import org.apache.spark.api.java.function.ForeachFunction;
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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 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.oa.graph.dump.skgif.beans.EmitPerManifestation;
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import eu.dnetlib.dhp.oa.graph.dump.skgif.beans.RelationPerProduct;
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import eu.dnetlib.dhp.skgif.model.*;
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import eu.dnetlib.dhp.utils.DHPUtils;
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/**
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* @author miriam.baglioni
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* @Date 20/02/24
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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.getLogger(DumpResultTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.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 testEmitFromResult() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/graph/")
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.getPath();
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final String workingDir = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/workingDir/")
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.getPath();
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DumpResult
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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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"-workingDir", workingDir
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<RelationPerProduct> relation = sc
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.textFile(workingDir + "/aggrelation")
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.map(item -> OBJECT_MAPPER.readValue(item, RelationPerProduct.class));
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Dataset<RelationPerProduct> relationDataset = spark
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.createDataset(relation.rdd(), Encoders.bean(RelationPerProduct.class));
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relationDataset.show(false);
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Assertions.assertEquals(7, relationDataset.count());
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RelationPerProduct temp = relationDataset
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.filter(
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(FilterFunction<RelationPerProduct>) r -> r
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.getResultId()
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.equalsIgnoreCase("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
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.first();
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Assertions
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.assertEquals(
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3, temp.getFunding().size() + temp.getRelatedProduct().size() + temp.getOrganizations().size());
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Assertions.assertEquals(1, temp.getFunding().size());
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Assertions.assertEquals(2, temp.getRelatedProduct().size());
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Assertions
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.assertEquals(
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1,
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temp
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.getRelatedProduct()
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.stream()
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.filter(rp -> rp.getRelation_type().equalsIgnoreCase("issupplementedby"))
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.count());
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Assertions
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.assertEquals(
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1,
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temp
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.getRelatedProduct()
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.stream()
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.filter(rp -> rp.getRelation_type().equalsIgnoreCase("isdocumentedby"))
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.count());
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JavaRDD<ResearchProduct> researchProduct = sc
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.textFile(workingDir.toString() + "/publication/researchproduct")
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.map(item -> OBJECT_MAPPER.readValue(item, ResearchProduct.class));
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org.apache.spark.sql.Dataset<ResearchProduct> researchProductDataset = spark
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.createDataset(researchProduct.rdd(), Encoders.bean(ResearchProduct.class));
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Assertions
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.assertEquals(
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1,
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researchProductDataset
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.filter(
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(FilterFunction<ResearchProduct>) p -> p
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.getLocal_identifier()
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.equalsIgnoreCase(
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Utils
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.getIdentifier(
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Prefixes.RESEARCH_PRODUCT,
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"50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")))
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.count());
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ResearchProduct product = researchProductDataset
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.filter(
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(FilterFunction<ResearchProduct>) p -> p
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.getLocal_identifier()
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.equalsIgnoreCase(
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Utils
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.getIdentifier(
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Prefixes.RESEARCH_PRODUCT, "50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")))
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.first();
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Assertions.assertEquals(2, product.getRelevant_organizations().size());
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Assertions.assertEquals(1, product.getFunding().size());
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Assertions.assertEquals(0, product.getRelated_products().size());
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Assertions.assertEquals(1, product.getContributions().size());
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Assertions.assertEquals(2, product.getManifestations().size());
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researchProductDataset.show(false);
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}
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@Test
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public void testEmitFromDedupedResult() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/graph_complete_entities/")
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.getPath();
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final String workingDir = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/skgif/workingDir_complete_entities/")
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.getPath();
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DumpResult
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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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"-workingDir", workingDir,
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"-outputPath", workingDir
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<ResearchProduct> researchProduct = sc
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.textFile(workingDir.toString() + "ResearchProduct")
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.map(item -> OBJECT_MAPPER.readValue(item, ResearchProduct.class));
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org.apache.spark.sql.Dataset<ResearchProduct> researchProductDataset = spark
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.createDataset(researchProduct.rdd(), Encoders.bean(ResearchProduct.class));
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Assertions.assertEquals(1, researchProductDataset.count());
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ResearchProduct rp = researchProductDataset.first();
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// check the local identifier
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Assertions.assertEquals("product_____::e22a152ab43b9215d14ece613f76ec84", rp.getLocal_identifier());
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// check the pids of the result
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Assertions.assertEquals(3, rp.getIdentifiers().size());
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Assertions
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.assertEquals(1, rp.getIdentifiers().stream().filter(p -> p.getScheme().equalsIgnoreCase("doi")).count());
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Assertions
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.assertEquals(
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"10.1007/s40199-021-00403-x",
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rp
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.getIdentifiers()
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.stream()
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.filter(p -> p.getScheme().equalsIgnoreCase("doi"))
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.collect(Collectors.toList())
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.get(0)
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.getValue());
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Assertions
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.assertEquals(1, rp.getIdentifiers().stream().filter(p -> p.getScheme().equalsIgnoreCase("pmid")).count());
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Assertions
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.assertEquals(
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"34327650",
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rp
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.getIdentifiers()
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.stream()
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.filter(p -> p.getScheme().equalsIgnoreCase("pmid"))
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.collect(Collectors.toList())
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.get(0)
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.getValue());
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Assertions
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.assertEquals(1, rp.getIdentifiers().stream().filter(p -> p.getScheme().equalsIgnoreCase("pmc")).count());
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Assertions
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.assertEquals(
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"PMC8602609",
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rp
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.getIdentifiers()
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.stream()
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.filter(p -> p.getScheme().equalsIgnoreCase("pmc"))
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.collect(Collectors.toList())
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.get(0)
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.getValue());
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// check the title
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Assertions.assertEquals(1, rp.getTitles().keySet().size());
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Assertions.assertTrue(rp.getTitles().keySet().contains("none"));
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Assertions.assertEquals(1, rp.getTitles().get("none").size());
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// check abstract
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Assertions.assertEquals(1, rp.getAbstracts().keySet().size());
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Assertions.assertTrue(rp.getAbstracts().keySet().contains("none"));
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Assertions.assertEquals(1, rp.getAbstracts().get("none").size());
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// check type
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Assertions.assertEquals("literature", rp.getProduct_type());
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// check topics
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Assertions.assertEquals(3, rp.getTopics().size());
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Assertions
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.assertTrue(
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rp
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.getTopics()
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.stream()
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.anyMatch(
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t -> t
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.getTopic()
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.getValue()
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.equalsIgnoreCase(Prefixes.TOPIC.label + DHPUtils.md5("FOSSustained delivery"))));
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// check contributions
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Assertions.assertEquals(4, rp.getContributions().size());
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Assertions
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.assertEquals(3, rp.getContributions().stream().filter(c -> c.getPerson().getLocal_identifier().startsWith("person")).count());
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Assertions
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.assertEquals(1, rp.getContributions().stream().filter(c -> c.getPerson().getLocal_identifier().startsWith("temp")).count());
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rp.getContributions().forEach(c -> Assertions.assertTrue(c.getDeclared_affiliation() == null));
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Assertions
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.assertEquals(
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1,
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rp
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.getContributions()
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.stream()
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.filter(c -> c.getPerson().equals(Utils.getIdentifier(Prefixes.PERSON, "0000-0001-8284-6269true")))
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.collect(Collectors.toList())
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.get(0)
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.getRank());
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Assertions
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.assertEquals(
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2,
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rp
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.getContributions()
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.stream()
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.filter(c -> c.getPerson().equals(Utils.getIdentifier(Prefixes.PERSON, "0000-0002-0940-893xtrue")))
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.collect(Collectors.toList())
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.get(0)
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.getRank());
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Assertions
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.assertEquals(
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3,
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rp
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.getContributions()
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.stream()
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.filter(c -> c.getPerson().equals(Utils.getIdentifier(Prefixes.PERSON, "0000-0001-5291-577xtrue")))
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.collect(Collectors.toList())
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.get(0)
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.getRank());
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Assertions
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.assertEquals(
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4,
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rp
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.getContributions()
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.stream()
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.filter(
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c -> c
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.getPerson()
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.equals(
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Utils
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.getIdentifier(
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Prefixes.TEMPORARY_PERSON,
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"50|doi_dedup___::0000661be7c602727bae9690778b16514")))
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.collect(Collectors.toList())
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.get(0)
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.getRank());
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researchProductDataset.show(10, 100, true);
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// check manifestation 1
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Assertions.assertEquals(3, rp.getManifestations().size());
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Manifestation manifestation = rp
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.getManifestations()
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.stream()
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.filter(
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m -> m
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.getHosting_datasource()
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.equals(
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Utils.getIdentifier(Prefixes.DATASOURCE, "10|doajarticles::6107489403b31fc7cf37cb7fda35f7f1")))
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.collect(Collectors.toList())
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.get(0);
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Assertions.assertEquals("Article", manifestation.getProduct_local_type());
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Assertions.assertEquals("dnet:publication_resource", manifestation.getProduct_local_type_schema());
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Assertions.assertEquals(1, manifestation.getDates().size());
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Assertions.assertEquals("2021-07-29", manifestation.getDates().get(0).getValue());
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Assertions.assertEquals("publishing", manifestation.getDates().get(0).getType());
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Assertions.assertEquals(PeerReview.PEER_REVIEWED.label, manifestation.getPeer_review());
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Assertions.assertEquals("unavailable", manifestation.getMetadata_curation());
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Assertions.assertEquals(AccessRight.CLOSED.label, manifestation.getAccess_right());
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Assertions.assertEquals("Springer Nature TDM", manifestation.getLicence());
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Assertions.assertEquals("https://doi.org/10.1007/s40199-021-00403-x", manifestation.getUrl());
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Assertions.assertEquals("10.1007/s40199-021-00403-x", manifestation.getPid());
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Assertions.assertTrue(manifestation.getBiblio() != null);
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Biblio biblio = manifestation.getBiblio();
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Assertions.assertTrue(biblio.getEdition() == null);
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Assertions.assertTrue(biblio.getIssue() == null);
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Assertions.assertEquals("Springer Science and Business Media LLC", biblio.getPublisher());
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Assertions.assertEquals("29", biblio.getVolume());
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Assertions.assertEquals("415", biblio.getStart_page());
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Assertions.assertEquals("438", biblio.getEnd_page());
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// check manifestation 2
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manifestation = rp
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.getManifestations()
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.stream()
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.filter(
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m -> m
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.getHosting_datasource()
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.equals(
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Utils.getIdentifier(Prefixes.DATASOURCE, "10|openaire____::55045bd2a65019fd8e6741a755395c8c")))
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.collect(Collectors.toList())
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.get(0);
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Assertions.assertEquals("Article", manifestation.getProduct_local_type());
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Assertions.assertEquals("dnet:publication_resource", manifestation.getProduct_local_type_schema());
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Assertions.assertEquals(1, manifestation.getDates().size());
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Assertions.assertEquals("2020-01-03", manifestation.getDates().get(0).getValue());
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Assertions.assertEquals("publishing", manifestation.getDates().get(0).getType());
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Assertions.assertEquals(PeerReview.NON_PEER_REVIEWED.label, manifestation.getPeer_review());
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Assertions.assertEquals("unavailable", manifestation.getMetadata_curation());
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Assertions.assertEquals(AccessRight.UNAVAILABLE.label, manifestation.getAccess_right());
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Assertions.assertEquals(null, manifestation.getLicence());
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Assertions.assertEquals("https://pubmed.ncbi.nlm.nih.gov/34327650", manifestation.getUrl());
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Assertions.assertEquals("34327650", manifestation.getPid());
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Assertions.assertTrue(manifestation.getBiblio() == null);
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// check manifestation 3
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manifestation = rp
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.getManifestations()
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.stream()
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.filter(
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m -> m
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.getHosting_datasource()
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.equals(
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Utils.getIdentifier(Prefixes.DATASOURCE, "10|opendoar____::8b6dd7db9af49e67306feb59a8bdc52c")))
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.collect(Collectors.toList())
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.get(0);
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Assertions.assertEquals("Other literature type", manifestation.getProduct_local_type());
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Assertions.assertEquals("dnet:publication_resource", manifestation.getProduct_local_type_schema());
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Assertions.assertEquals(1, manifestation.getDates().size());
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Assertions.assertEquals("2021-07-29", manifestation.getDates().get(0).getValue());
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Assertions.assertEquals("publishing", manifestation.getDates().get(0).getType());
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Assertions.assertEquals(PeerReview.NON_PEER_REVIEWED.label, manifestation.getPeer_review());
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Assertions.assertEquals("unavailable", manifestation.getMetadata_curation());
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Assertions.assertEquals(AccessRight.OPEN.label, manifestation.getAccess_right());
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Assertions.assertEquals(null, manifestation.getLicence());
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Assertions.assertEquals("https://europepmc.org/articles/PMC8602609/", manifestation.getUrl());
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Assertions.assertEquals("PMC8602609", manifestation.getPid());
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Assertions.assertTrue(manifestation.getBiblio() == null);
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// check relevant organization
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Assertions.assertEquals(1, rp.getRelevant_organizations().size());
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Assertions
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.assertEquals(
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Prefixes.ORGANIZATION.label + "601e510b1fda7cc6cb03329531502171",
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rp.getRelevant_organizations().get(0));
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// check funding
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Assertions.assertEquals(1, rp.getFunding().size());
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Assertions.assertEquals(Prefixes.GRANT.label + "a7795022763d413f5de59036ebbd0c52", rp.getFunding().get(0));
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// check related products
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Assertions.assertEquals(5, rp.getRelated_products().size());
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Assertions
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.assertEquals(
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4,
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rp
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.getRelated_products()
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.stream()
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.filter(r -> r.getRelation_type().equalsIgnoreCase(RelationType.CITATION.label))
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.collect(Collectors.toList())
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.get(0)
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.getProduct_list()
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.size());
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Assertions
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.assertEquals(
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1,
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rp
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.getRelated_products()
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.stream()
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.filter(r -> r.getRelation_type().equalsIgnoreCase(RelationType.DOCUMENTS.label))
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.collect(Collectors.toList())
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.get(0)
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.getProduct_list()
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.size());
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Assertions
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.assertEquals(
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1,
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rp
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.getRelated_products()
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.stream()
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.filter(r -> r.getRelation_type().equalsIgnoreCase(RelationType.PART.label))
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.collect(Collectors.toList())
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.get(0)
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.getProduct_list()
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.size());
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Assertions
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.assertEquals(
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1,
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rp
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.getRelated_products()
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.stream()
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.filter(r -> r.getRelation_type().equalsIgnoreCase(RelationType.SUPPLEMENT.label))
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.collect(Collectors.toList())
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.get(0)
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.getProduct_list()
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.size());
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Assertions
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.assertEquals(
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1,
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rp
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.getRelated_products()
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.stream()
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.filter(r -> r.getRelation_type().equalsIgnoreCase(RelationType.VERSION.label))
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.collect(Collectors.toList())
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.get(0)
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.getProduct_list()
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.size());
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}
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}
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