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1014 lines
36 KiB
Java
1014 lines
36 KiB
Java
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package eu.dnetlib.dhp.oa.graph.dump;
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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.Arrays;
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import java.util.List;
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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.sql.Encoders;
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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 com.fasterxml.jackson.core.JsonProcessingException;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.Gson;
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import eu.dnetlib.dhp.eosc.model.EoscResult;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.oa.graph.dump.eosc.SelectEoscResultsJobStep1;
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import eu.dnetlib.dhp.oa.model.Instance;
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import eu.dnetlib.dhp.oa.model.OpenAccessRoute;
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import eu.dnetlib.dhp.oa.model.community.CommunityResult;
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import eu.dnetlib.dhp.oa.model.graph.GraphResult;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.Dataset;
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import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Software;
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//@Disabled
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public class DumpJobTest {
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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(DumpJobTest.class);
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private static final CommunityMap map = new CommunityMap();
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static {
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map.put("egi", "EGI Federation");
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map.put("fet-fp7", "FET FP7");
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map.put("fet-h2020", "FET H2020");
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map.put("clarin", "CLARIN");
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map.put("fam", "Fisheries and Aquaculture Management");
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map.put("ni", "Neuroinformatics");
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map.put("mes", "European Marine Scinece");
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map.put("instruct", "Instruct-Eric");
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map.put("rda", "Research Data Alliance");
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map.put("elixir-gr", "ELIXIR GR");
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map.put("aginfra", "Agricultural and Food Sciences");
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map.put("dariah", "DARIAH EU");
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map.put("risis", "RISI");
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map.put("ee", "SDSN - Greece");
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map.put("oa-pg", "EC Post-Grant Open Access Pilot");
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map.put("beopen", "Transport Research");
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map.put("euromarine", "Euromarine");
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map.put("ifremer", "Ifremer");
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map.put("dh-ch", "Digital Humanities and Cultural Heritage");
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map.put("science-innovation-policy", "Science and Innovation Policy Studies");
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map.put("covid-19", "COVID-19");
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map.put("enrmaps", "Energy Research");
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map.put("epos", "EPOS");
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}
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List<String> communityMap = Arrays
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.asList(
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"<community id=\"egi\" label=\"EGI Federation\"/>",
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"<community id=\"fet-fp7\" label=\"FET FP7\"/>",
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"<community id=\"fet-h2020\" label=\"FET H2020\"/>",
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"<community id=\"clarin\" label=\"CLARIN\"/>",
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"<community id=\"rda\" label=\"Research Data Alliance\"/>",
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"<community id=\"ee\" label=\"SDSN - Greece\"/>",
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"<community id=\"dh-ch\" label=\"Digital Humanities and Cultural Heritage\"/>",
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"<community id=\"fam\" label=\"Fisheries and Aquaculture Management\"/>",
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"<community id=\"ni\" label=\"Neuroinformatics\"/>",
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"<community id=\"mes\" label=\"European Marine Science\"/>",
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"<community id=\"instruct\" label=\"Instruct-ERIC\"/>",
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"<community id=\"elixir-gr\" label=\"ELIXIR GR\"/>",
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"<community id=\"aginfra\" label=\"Agricultural and Food Sciences\"/>",
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"<community id=\"dariah\" label=\"DARIAH EU\"/>",
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"<community id=\"risis\" label=\"RISIS\"/>",
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"<community id=\"epos\" label=\"EPOS\"/>",
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"<community id=\"beopen\" label=\"Transport Research\"/>",
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"<community id=\"euromarine\" label=\"EuroMarine\"/>",
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"<community id=\"ifremer\" label=\"Ifremer\"/>",
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"<community id=\"oa-pg\" label=\"EC Post-Grant Open Access Pilot\"/>",
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"<community id=\"science-innovation-policy\" label=\"Science and Innovation Policy Studies\"/>",
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"<community id=\"covid-19\" label=\"COVID-19\"/>",
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"<community id=\"enermaps\" label=\"Energy Research\"/>");
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private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') "
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+
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" where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " +
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" return " +
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"<community> " +
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"{$x//CONFIGURATION/context/@id}" +
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"{$x//CONFIGURATION/context/@label}" +
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"</community>";
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(DumpJobTest.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(DumpJobTest.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(DumpJobTest.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 testMap() {
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System.out.println(new Gson().toJson(map));
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}
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@Test
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public void testPublicationDump() {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance")
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.getPath();
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final String communityMapPath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
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.getPath();
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DumpProducts dump = new DumpProducts();
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dump
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.run(
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// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
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false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
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GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<GraphResult> tmp = sc
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.textFile(workingDir.toString() + "/result")
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.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
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org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
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Assertions.assertEquals(1, verificationDataset.count());
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GraphResult gr = verificationDataset.first();
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Assertions.assertEquals(6, gr.getAuthor().size());
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Assertions
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.assertTrue(
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gr
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.getAuthor()
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.stream()
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.anyMatch(
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a -> a.getFullname().equals("Nikolaidou,Charitini") &&
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a.getName().equals("Charitini") && a.getSurname().equals("Nikolaidou")
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&& a.getRank() == 1 && a.getPid() == null));
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Assertions
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.assertTrue(
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gr
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.getAuthor()
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.stream()
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.anyMatch(
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a -> a.getFullname().equals("Votsi,Nefta") &&
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a.getName().equals("Nefta") && a.getSurname().equals("Votsi")
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&& a.getRank() == 2 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID)
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&& a.getPid().getId().getValue().equals("0000-0001-6651-1178")
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&& a.getPid().getProvenance() != null));
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Assertions
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.assertTrue(
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gr
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.getAuthor()
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.stream()
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.anyMatch(
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a -> a.getFullname().equals("Sgardelis,Steanos") &&
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a.getName().equals("Steanos") && a.getSurname().equals("Sgardelis")
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&& a.getRank() == 3 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING)
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&& a.getPid().getId().getValue().equals("0000-0001-6651-1178")
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&& a.getPid().getProvenance() != null));
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Assertions
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.assertTrue(
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gr
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.getAuthor()
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.stream()
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.anyMatch(
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a -> a.getFullname().equals("Halley,John") &&
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a.getName().equals("John") && a.getSurname().equals("Halley")
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&& a.getRank() == 4 && a.getPid() == null));
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Assertions
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.assertTrue(
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gr
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.getAuthor()
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.stream()
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.anyMatch(
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a -> a.getFullname().equals("Pantis,John") &&
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a.getName().equals("John") && a.getSurname().equals("Pantis")
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&& a.getRank() == 5 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID)
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&& a.getPid().getId().getValue().equals("0000-0001-6651-1178")
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&& a.getPid().getProvenance() != null));
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Assertions
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.assertTrue(
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gr
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.getAuthor()
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.stream()
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.anyMatch(
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a -> a.getFullname().equals("Tsiafouli,Maria") &&
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a.getName().equals("Maria") && a.getSurname().equals("Tsiafouli")
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&& a.getRank() == 6 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING)
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&& a.getPid().getId().getValue().equals("0000-0001-6651-1178")
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&& a.getPid().getProvenance() != null));
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Assertions.assertEquals("publication", gr.getType());
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Assertions.assertEquals("eng", gr.getLanguage().getCode());
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Assertions.assertEquals("English", gr.getLanguage().getLabel());
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Assertions.assertEquals(1, gr.getCountry().size());
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Assertions.assertEquals("IT", gr.getCountry().get(0).getCode());
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Assertions.assertEquals("Italy", gr.getCountry().get(0).getLabel());
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Assertions.assertTrue(gr.getCountry().get(0).getProvenance() == null);
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Assertions.assertEquals(12, gr.getSubjects().size());
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Assertions
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.assertTrue(
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gr
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.getSubjects()
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.stream()
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.anyMatch(
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s -> s.getSubject().getValue().equals("Ecosystem Services hotspots")
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&& s.getSubject().getScheme().equals("ACM") && s.getProvenance() != null &&
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s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository")));
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Assertions
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.assertTrue(
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gr
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.getSubjects()
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.stream()
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.anyMatch(
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s -> s.getSubject().getValue().equals("Natura 2000")
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&& s.getSubject().getScheme().equals("") && s.getProvenance() != null &&
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s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository")));
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Assertions
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.assertEquals(
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"Ecosystem Service capacity is higher in areas of multiple designation types",
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gr.getMaintitle());
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Assertions.assertEquals(null, gr.getSubtitle());
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Assertions.assertEquals(1, gr.getDescription().size());
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Assertions
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.assertTrue(
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gr
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.getDescription()
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.get(0)
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.startsWith("The implementation of the Ecosystem Service (ES) concept into practice"));
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Assertions
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.assertTrue(
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gr
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.getDescription()
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.get(0)
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.endsWith(
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"start complying with new standards and demands for nature conservation and environmental management."));
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Assertions.assertEquals("2017-01-01", gr.getPublicationdate());
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Assertions.assertEquals("Pensoft Publishers", gr.getPublisher());
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Assertions.assertEquals(null, gr.getEmbargoenddate());
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Assertions.assertEquals(1, gr.getSource().size());
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Assertions.assertEquals("One Ecosystem 2: e13718", gr.getSource().get(0));
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Assertions.assertEquals(1, gr.getFormat().size());
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Assertions.assertEquals("text/html", gr.getFormat().get(0));
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Assertions.assertEquals(0, gr.getContributor().size());
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Assertions.assertEquals(0, gr.getCoverage().size());
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Assertions.assertEquals(ModelConstants.ACCESS_RIGHT_OPEN, gr.getBestaccessright().getLabel());
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Assertions
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.assertEquals(
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Constants.accessRightsCoarMap.get(ModelConstants.ACCESS_RIGHT_OPEN), gr.getBestaccessright().getCode());
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Assertions.assertEquals("One Ecosystem", gr.getContainer().getName());
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Assertions.assertEquals("2367-8194", gr.getContainer().getIssnOnline());
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Assertions.assertEquals("", gr.getContainer().getIssnPrinted());
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Assertions.assertEquals("", gr.getContainer().getIssnLinking());
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Assertions.assertTrue(null == gr.getDocumentationUrl() || gr.getDocumentationUrl().size() == 0);
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Assertions.assertTrue(null == gr.getCodeRepositoryUrl());
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Assertions.assertEquals(null, gr.getProgrammingLanguage());
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Assertions.assertTrue(null == gr.getContactperson() || gr.getContactperson().size() == 0);
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Assertions.assertTrue(null == gr.getContactgroup() || gr.getContactgroup().size() == 0);
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Assertions.assertTrue(null == gr.getTool() || gr.getTool().size() == 0);
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Assertions.assertEquals(null, gr.getSize());
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Assertions.assertEquals(null, gr.getVersion());
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Assertions.assertTrue(null == gr.getGeolocation() || gr.getGeolocation().size() == 0);
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Assertions.assertEquals("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId());
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Assertions.assertEquals(1, gr.getOriginalId().size());
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Assertions
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.assertTrue(
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gr.getOriginalId().contains("10.3897/oneeco.2.e13718"));
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Assertions.assertEquals(1, gr.getPid().size());
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Assertions
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.assertTrue(
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gr.getPid().get(0).getScheme().equals("doi")
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&& gr.getPid().get(0).getValue().equals("10.1016/j.triboint.2014.05.004"));
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Assertions.assertEquals("2020-03-23T00:20:51.392Z", gr.getDateofcollection());
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Assertions.assertEquals(1, gr.getInstance().size());
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Instance instance = gr.getInstance().get(0);
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Assertions.assertEquals(0, instance.getPid().size());
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Assertions.assertEquals(1, instance.getAlternateIdentifier().size());
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Assertions
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.assertTrue(
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instance.getAlternateIdentifier().get(0).getScheme().equals("doi")
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&& instance.getAlternateIdentifier().get(0).getValue().equals("10.3897/oneeco.2.e13718"));
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Assertions.assertEquals(null, instance.getLicense());
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Assertions
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.assertTrue(
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instance
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.getAccessright()
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.getCode()
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.equals(
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Constants.accessRightsCoarMap
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.get(ModelConstants.ACCESS_RIGHT_OPEN)));
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Assertions.assertTrue(instance.getAccessright().getLabel().equals(ModelConstants.ACCESS_RIGHT_OPEN));
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Assertions.assertTrue(instance.getAccessright().getOpenAccessRoute().equals(OpenAccessRoute.green));
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Assertions.assertTrue(instance.getType().equals("Article"));
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Assertions.assertEquals(2, instance.getUrl().size());
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Assertions
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.assertTrue(
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instance.getUrl().contains("https://doi.org/10.3897/oneeco.2.e13718")
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&& instance.getUrl().contains("https://oneecosystem.pensoft.net/article/13718/"));
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Assertions.assertEquals("2017-01-01", instance.getPublicationdate());
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Assertions.assertEquals(null, instance.getArticleprocessingcharge());
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Assertions.assertEquals("peerReviewed", instance.getRefereed());
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}
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@Test
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public void testDatasetDump() {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance")
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.getPath();
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final String communityMapPath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
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.getPath();
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DumpProducts dump = new DumpProducts();
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dump
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.run(
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false, sourcePath, workingDir.toString() + "/result",
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communityMapPath, Dataset.class,
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GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<GraphResult> tmp = sc
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.textFile(workingDir.toString() + "/result")
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.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
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org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
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Assertions.assertEquals(1, verificationDataset.count());
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Assertions.assertEquals(1, verificationDataset.filter("type = 'dataset'").count());
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// the common fields in the result have been already checked. Now checking only
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// community specific fields
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GraphResult gr = verificationDataset.first();
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Assertions.assertEquals(2, gr.getGeolocation().size());
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Assertions.assertEquals(2, gr.getGeolocation().stream().filter(gl -> gl.getBox().equals("")).count());
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Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPlace().equals("")).count());
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Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("")).count());
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Assertions
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.assertEquals(
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1,
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gr
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.getGeolocation()
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.stream()
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.filter(gl -> gl.getPlace().equals("18 York St, Ottawa, ON K1N 5S6; Ottawa; Ontario; Canada"))
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.count());
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Assertions
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.assertEquals(
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1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("45.427242 -75.693904")).count());
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Assertions
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.assertEquals(
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1,
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gr
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.getGeolocation()
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.stream()
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.filter(gl -> gl.getPoint().equals("") && !gl.getPlace().equals(""))
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.count());
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Assertions
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.assertEquals(
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1,
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gr
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.getGeolocation()
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.stream()
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.filter(gl -> !gl.getPoint().equals("") && gl.getPlace().equals(""))
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.count());
|
|
|
|
Assertions.assertEquals("1024Gb", gr.getSize());
|
|
|
|
Assertions.assertEquals("1.01", gr.getVersion());
|
|
|
|
Assertions.assertEquals(null, gr.getContainer());
|
|
Assertions.assertEquals(null, gr.getCodeRepositoryUrl());
|
|
Assertions.assertEquals(null, gr.getProgrammingLanguage());
|
|
Assertions.assertEquals(null, gr.getDocumentationUrl());
|
|
Assertions.assertEquals(null, gr.getContactperson());
|
|
Assertions.assertEquals(null, gr.getContactgroup());
|
|
Assertions.assertEquals(null, gr.getTool());
|
|
|
|
}
|
|
|
|
@Test
|
|
public void testSoftwareDump() {
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software_extendedinstance")
|
|
.getPath();
|
|
|
|
final String communityMapPath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
|
|
.getPath();
|
|
|
|
DumpProducts dump = new DumpProducts();
|
|
dump
|
|
.run(
|
|
false, sourcePath, workingDir.toString() + "/result",
|
|
communityMapPath, Software.class,
|
|
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<GraphResult> tmp = sc
|
|
.textFile(workingDir.toString() + "/result")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
|
|
|
|
org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
|
|
.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
|
|
|
|
Assertions.assertEquals(1, verificationDataset.count());
|
|
|
|
Assertions.assertEquals(1, verificationDataset.filter("type = 'software'").count());
|
|
|
|
GraphResult gr = verificationDataset.first();
|
|
|
|
Assertions.assertEquals(2, gr.getDocumentationUrl().size());
|
|
Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_1"));
|
|
Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_2"));
|
|
|
|
Assertions.assertEquals("code_repo", gr.getCodeRepositoryUrl());
|
|
|
|
Assertions.assertEquals("perl", gr.getProgrammingLanguage());
|
|
|
|
Assertions.assertEquals(null, gr.getContainer());
|
|
Assertions.assertEquals(null, gr.getContactperson());
|
|
Assertions.assertEquals(null, gr.getContactgroup());
|
|
Assertions.assertEquals(null, gr.getTool());
|
|
Assertions.assertEquals(null, gr.getGeolocation());
|
|
Assertions.assertEquals(null, gr.getSize());
|
|
Assertions.assertEquals(null, gr.getVersion());
|
|
|
|
}
|
|
|
|
@Test
|
|
public void testOrpDump() {
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp_extendedinstance")
|
|
.getPath();
|
|
|
|
final String communityMapPath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
|
|
.getPath();
|
|
|
|
DumpProducts dump = new DumpProducts();
|
|
dump
|
|
.run(
|
|
false, sourcePath, workingDir.toString() + "/result",
|
|
communityMapPath, OtherResearchProduct.class,
|
|
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<GraphResult> tmp = sc
|
|
.textFile(workingDir.toString() + "/result")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
|
|
|
|
org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
|
|
.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
|
|
|
|
Assertions.assertEquals(1, verificationDataset.count());
|
|
|
|
Assertions.assertEquals(1, verificationDataset.filter("type = 'other'").count());
|
|
|
|
GraphResult gr = verificationDataset.first();
|
|
|
|
Assertions.assertEquals(2, gr.getContactperson().size());
|
|
Assertions.assertTrue(gr.getContactperson().contains(("contact_person1")));
|
|
Assertions.assertTrue(gr.getContactperson().contains(("contact_person2")));
|
|
|
|
Assertions.assertEquals(1, gr.getContactgroup().size());
|
|
Assertions.assertTrue(gr.getContactgroup().contains(("contact_group")));
|
|
|
|
Assertions.assertEquals(2, gr.getTool().size());
|
|
Assertions.assertTrue(gr.getTool().contains("tool1"));
|
|
Assertions.assertTrue(gr.getTool().contains("tool2"));
|
|
|
|
Assertions.assertEquals(null, gr.getContainer());
|
|
Assertions.assertEquals(null, gr.getDocumentationUrl());
|
|
Assertions.assertEquals(null, gr.getCodeRepositoryUrl());
|
|
Assertions.assertEquals(null, gr.getProgrammingLanguage());
|
|
Assertions.assertEquals(null, gr.getGeolocation());
|
|
Assertions.assertEquals(null, gr.getSize());
|
|
Assertions.assertEquals(null, gr.getVersion());
|
|
|
|
}
|
|
|
|
@Test
|
|
public void testPublicationDumpCommunity() throws JsonProcessingException {
|
|
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance")
|
|
.getPath();
|
|
|
|
final String communityMapPath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
|
|
.getPath();
|
|
|
|
DumpProducts dump = new DumpProducts();
|
|
dump
|
|
.run(
|
|
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
|
|
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<CommunityResult> tmp = sc
|
|
.textFile(workingDir.toString() + "/result")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
|
|
|
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
|
|
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
|
|
|
|
Assertions.assertEquals(1, verificationDataset.count());
|
|
|
|
Assertions.assertEquals(1, verificationDataset.filter("type = 'publication'").count());
|
|
|
|
// the common fields in the result have been already checked. Now checking only
|
|
// community specific fields
|
|
|
|
CommunityResult cr = verificationDataset.first();
|
|
|
|
Assertions.assertEquals(1, cr.getContext().size());
|
|
Assertions.assertEquals("dh-ch", cr.getContext().get(0).getCode());
|
|
Assertions.assertEquals("Digital Humanities and Cultural Heritage", cr.getContext().get(0).getLabel());
|
|
Assertions.assertEquals(1, cr.getContext().get(0).getProvenance().size());
|
|
Assertions.assertEquals("Inferred by OpenAIRE", cr.getContext().get(0).getProvenance().get(0).getProvenance());
|
|
Assertions.assertEquals("0.9", cr.getContext().get(0).getProvenance().get(0).getTrust());
|
|
|
|
Assertions.assertEquals(1, cr.getCollectedfrom().size());
|
|
Assertions
|
|
.assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getCollectedfrom().get(0).getKey());
|
|
Assertions.assertEquals("Pensoft", cr.getCollectedfrom().get(0).getValue());
|
|
|
|
Assertions.assertEquals(1, cr.getInstance().size());
|
|
Assertions
|
|
.assertEquals(
|
|
"10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db",
|
|
cr.getInstance().get(0).getCollectedfrom().getKey());
|
|
Assertions.assertEquals("Pensoft", cr.getInstance().get(0).getCollectedfrom().getValue());
|
|
Assertions
|
|
.assertEquals(
|
|
"10|openaire____::e707e544b9a5bd23fc27fbfa65eb60dd", cr.getInstance().get(0).getHostedby().getKey());
|
|
Assertions.assertEquals("One Ecosystem", cr.getInstance().get(0).getHostedby().getValue());
|
|
|
|
}
|
|
|
|
@Test
|
|
public void testDataset() {
|
|
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset.json")
|
|
.getPath();
|
|
|
|
final String communityMapPath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
|
|
.getPath();
|
|
|
|
DumpProducts dump = new DumpProducts();
|
|
dump
|
|
.run(
|
|
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
|
|
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<CommunityResult> tmp = sc
|
|
.textFile(workingDir.toString() + "/result")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
|
|
|
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
|
|
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
|
|
|
|
Assertions.assertEquals(90, verificationDataset.count());
|
|
|
|
Assertions
|
|
.assertTrue(
|
|
verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset
|
|
.filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'")
|
|
.count());
|
|
|
|
Assertions
|
|
.assertTrue(
|
|
verificationDataset.filter("bestAccessright.code = 'c_16ec'").count() == verificationDataset
|
|
.filter("bestAccessright.code = 'c_16ec' and bestAccessright.label = 'RESTRICTED'")
|
|
.count());
|
|
|
|
Assertions
|
|
.assertTrue(
|
|
verificationDataset.filter("bestAccessright.code = 'c_14cb'").count() == verificationDataset
|
|
.filter("bestAccessright.code = 'c_14cb' and bestAccessright.label = 'CLOSED'")
|
|
.count());
|
|
|
|
Assertions
|
|
.assertTrue(
|
|
verificationDataset.filter("bestAccessright.code = 'c_f1cf'").count() == verificationDataset
|
|
.filter("bestAccessright.code = 'c_f1cf' and bestAccessright.label = 'EMBARGO'")
|
|
.count());
|
|
|
|
Assertions.assertTrue(verificationDataset.filter("size(context) > 0").count() == 90);
|
|
|
|
Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90);
|
|
|
|
}
|
|
|
|
@Test
|
|
public void testDataset2All() {
|
|
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned")
|
|
.getPath();
|
|
|
|
final String communityMapPath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
|
|
.getPath();
|
|
|
|
DumpProducts dump = new DumpProducts();
|
|
dump
|
|
.run(
|
|
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
|
|
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
|
|
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<GraphResult> tmp = sc
|
|
.textFile(workingDir.toString() + "/result")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
|
|
|
|
org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
|
|
.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
|
|
|
|
Assertions.assertEquals(5, verificationDataset.count());
|
|
|
|
}
|
|
|
|
@Test
|
|
public void testDataset2Communities() {
|
|
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned")
|
|
.getPath();
|
|
|
|
final String communityMapPath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
|
|
.getPath();
|
|
|
|
DumpProducts dump = new DumpProducts();
|
|
dump
|
|
.run(
|
|
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
|
|
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<CommunityResult> tmp = sc
|
|
.textFile(workingDir.toString() + "/result")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
|
|
|
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
|
|
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
|
|
|
|
Assertions.assertEquals(0, verificationDataset.count());
|
|
|
|
}
|
|
|
|
@Test
|
|
public void testPublication() {
|
|
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication.json")
|
|
.getPath();
|
|
|
|
final String communityMapPath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
|
|
.getPath();
|
|
|
|
DumpProducts dump = new DumpProducts();
|
|
dump
|
|
.run(
|
|
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
|
|
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
|
|
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<CommunityResult> tmp = sc
|
|
.textFile(workingDir.toString() + "/result")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
|
|
|
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
|
|
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
|
|
|
|
Assertions.assertEquals(74, verificationDataset.count());
|
|
verificationDataset.show(false);
|
|
|
|
Assertions.assertEquals(74, verificationDataset.filter("type = 'publication'").count());
|
|
|
|
}
|
|
|
|
@Test
|
|
public void testSoftware() {
|
|
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software.json")
|
|
.getPath();
|
|
|
|
final String communityMapPath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
|
|
.getPath();
|
|
|
|
DumpProducts dump = new DumpProducts();
|
|
dump
|
|
.run(
|
|
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class,
|
|
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class,
|
|
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<CommunityResult> tmp = sc
|
|
.textFile(workingDir.toString() + "/result")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
|
|
|
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
|
|
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
|
|
|
|
Assertions.assertEquals(6, verificationDataset.count());
|
|
|
|
Assertions.assertEquals(6, verificationDataset.filter("type = 'software'").count());
|
|
|
|
}
|
|
|
|
@Test
|
|
public void testORP() {
|
|
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp.json")
|
|
.getPath();
|
|
|
|
final String communityMapPath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
|
|
.getPath();
|
|
|
|
DumpProducts dump = new DumpProducts();
|
|
dump
|
|
.run(
|
|
// false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class,
|
|
false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class,
|
|
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<CommunityResult> tmp = sc
|
|
.textFile(workingDir.toString() + "/result")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
|
|
|
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
|
|
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
|
|
|
|
Assertions.assertEquals(3, verificationDataset.count());
|
|
|
|
Assertions.assertEquals(3, verificationDataset.filter("type = 'other'").count());
|
|
|
|
}
|
|
|
|
@Test
|
|
public void testRecord() {
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/singelRecord_pub.json")
|
|
.getPath();
|
|
|
|
final String communityMapPath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
|
|
.getPath();
|
|
|
|
DumpProducts dump = new DumpProducts();
|
|
dump
|
|
.run(
|
|
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
|
|
CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<CommunityResult> tmp = sc
|
|
.textFile(workingDir.toString() + "/result")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
|
|
|
org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
|
|
.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
|
|
|
|
Assertions.assertEquals(2, verificationDataset.count());
|
|
verificationDataset.show(false);
|
|
|
|
Assertions.assertEquals(2, verificationDataset.filter("type = 'publication'").count());
|
|
|
|
}
|
|
|
|
@Test
|
|
public void testEOSCDump() throws Exception {
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/eosc/eosctag.json")
|
|
.getPath();
|
|
|
|
final String communityMapPath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
|
|
.getPath();
|
|
|
|
SelectEoscResultsJobStep1
|
|
.main(
|
|
new String[] {
|
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
|
"-sourcePath",
|
|
sourcePath,
|
|
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
|
"-outputPath", workingDir.toString() + "/working"
|
|
|
|
});
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<EoscResult> tmp = sc
|
|
.textFile(workingDir.toString() + "/working")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, EoscResult.class));
|
|
|
|
org.apache.spark.sql.Dataset<EoscResult> verificationDataset = spark
|
|
.createDataset(tmp.rdd(), Encoders.bean(EoscResult.class));
|
|
|
|
Assertions.assertEquals(1, verificationDataset.count());
|
|
|
|
Assertions.assertEquals(1, verificationDataset.filter("type = 'dataset'").count());
|
|
|
|
Assertions.assertEquals(1, tmp.filter(d -> d.getEoscIF().getCode().equals("EOSC::Twitter Data")).count());
|
|
Assertions.assertEquals(1, tmp.filter(d -> d.getEoscIF().getLabel().equals("EOSC::Twitter Data")).count());
|
|
Assertions.assertEquals(1, tmp.filter(d -> d.getEoscIF().getUrl().equals("")).count());
|
|
Assertions.assertEquals(1, tmp.filter(d -> d.getEoscIF().getSemanticRelation().equals("compliesWith")).count());
|
|
|
|
}
|
|
|
|
@Test
|
|
public void testArticlePCA() {
|
|
final String sourcePath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_pca")
|
|
.getPath();
|
|
|
|
final String communityMapPath = getClass()
|
|
.getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json")
|
|
.getPath();
|
|
|
|
DumpProducts dump = new DumpProducts();
|
|
dump
|
|
.run(
|
|
false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class,
|
|
GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType());
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
JavaRDD<GraphResult> tmp = sc
|
|
.textFile(workingDir.toString() + "/result")
|
|
.map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class));
|
|
|
|
org.apache.spark.sql.Dataset<GraphResult> verificationDataset = spark
|
|
.createDataset(tmp.rdd(), Encoders.bean(GraphResult.class));
|
|
|
|
Assertions.assertEquals(23, verificationDataset.count());
|
|
|
|
Assertions.assertEquals(23, verificationDataset.filter("type = 'publication'").count());
|
|
|
|
verificationDataset.createOrReplaceTempView("check");
|
|
|
|
org.apache.spark.sql.Dataset<Row> temp = spark
|
|
.sql(
|
|
"select id " +
|
|
"from check " +
|
|
"lateral view explode (instance) i as inst " +
|
|
"where inst.articleprocessingcharge is not null");
|
|
|
|
Assertions.assertTrue(temp.count() == 2);
|
|
|
|
Assertions.assertTrue(temp.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'").count() == 1);
|
|
|
|
Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1);
|
|
|
|
temp = spark
|
|
.sql(
|
|
"select id, inst.articleprocessingcharge.amount, inst.articleprocessingcharge.currency " +
|
|
"from check " +
|
|
"lateral view explode (instance) i as inst " +
|
|
"where inst.articleprocessingcharge is not null");
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
"3131.64",
|
|
temp
|
|
.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'")
|
|
.collectAsList()
|
|
.get(0)
|
|
.getString(1));
|
|
Assertions
|
|
.assertEquals(
|
|
"EUR",
|
|
temp
|
|
.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'")
|
|
.collectAsList()
|
|
.get(0)
|
|
.getString(2));
|
|
|
|
Assertions
|
|
.assertEquals(
|
|
"2578.35",
|
|
temp
|
|
.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'")
|
|
.collectAsList()
|
|
.get(0)
|
|
.getString(1));
|
|
Assertions
|
|
.assertEquals(
|
|
"EUR",
|
|
temp
|
|
.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'")
|
|
.collectAsList()
|
|
.get(0)
|
|
.getString(2));
|
|
}
|
|
|
|
}
|