412 lines
15 KiB
Java
412 lines
15 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.api.java.function.ForeachFunction;
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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.*;
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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 com.google.gson.Gson;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
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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 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 testDataset() {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset.json")
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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, Dataset.class,
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false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
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CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<CommunityResult> tmp = sc
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.textFile(workingDir.toString() + "/result")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
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Assertions.assertEquals(90, verificationDataset.count());
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// verificationDataset
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// .filter("id = '50|DansKnawCris::1a960e20087cb46b93588e4e184e8a58'")
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// .foreach((ForeachFunction<CommunityResult>) rec -> System.out.println(OBJECT_MAPPER.writeValueAsString(rec)));
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Assertions
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.assertTrue(
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verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset
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.filter("bestAccessright.code = 'c_abf2' and bestAccessright.label = 'OPEN'")
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.count());
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Assertions
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.assertTrue(
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verificationDataset.filter("bestAccessright.code = 'c_16ec'").count() == verificationDataset
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.filter("bestAccessright.code = 'c_16ec' and bestAccessright.label = 'RESTRICTED'")
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.count());
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Assertions
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.assertTrue(
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verificationDataset.filter("bestAccessright.code = 'c_14cb'").count() == verificationDataset
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.filter("bestAccessright.code = 'c_14cb' and bestAccessright.label = 'CLOSED'")
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.count());
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Assertions
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.assertTrue(
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verificationDataset.filter("bestAccessright.code = 'c_f1cf'").count() == verificationDataset
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.filter("bestAccessright.code = 'c_f1cf' and bestAccessright.label = 'EMBARGO'")
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.count());
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Assertions.assertTrue(verificationDataset.filter("size(context) > 0").count() == 90);
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Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90);
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//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
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}
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@Test
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public void testDataset2All() {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned")
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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, Dataset.class,
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false, sourcePath, workingDir.toString() + "/result", 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<eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult> tmp = sc
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.textFile(workingDir.toString() + "/result")
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.map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult.class));
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org.apache.spark.sql.Dataset<eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult.class));
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Assertions.assertEquals(5, verificationDataset.count());
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verificationDataset
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.foreach((ForeachFunction<GraphResult>) res -> System.out.println(OBJECT_MAPPER.writeValueAsString(res)));
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}
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@Test
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public void testDataset2Communities() {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_cleaned")
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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, Dataset.class,
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false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class,
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CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<CommunityResult> tmp = sc
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.textFile(workingDir.toString() + "/result")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
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Assertions.assertEquals(0, verificationDataset.count());
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verificationDataset.show(false);
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}
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@Test
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public void testPublication() {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication.json")
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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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CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<CommunityResult> tmp = sc
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.textFile(workingDir.toString() + "/result")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
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Assertions.assertEquals(74, verificationDataset.count());
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verificationDataset.show(false);
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Assertions.assertEquals(74, verificationDataset.filter("type = 'publication'").count());
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//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
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}
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@Test
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public void testSoftware() {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software.json")
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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, Software.class,
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false, sourcePath, workingDir.toString() + "/result", communityMapPath, Software.class,
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CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<CommunityResult> tmp = sc
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.textFile(workingDir.toString() + "/result")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
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Assertions.assertEquals(6, verificationDataset.count());
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Assertions.assertEquals(6, verificationDataset.filter("type = 'software'").count());
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verificationDataset.show(false);
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//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
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}
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@Test
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public void testORP() {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp.json")
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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, OtherResearchProduct.class,
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false, sourcePath, workingDir.toString() + "/result", communityMapPath, OtherResearchProduct.class,
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CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<CommunityResult> tmp = sc
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.textFile(workingDir.toString() + "/result")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
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Assertions.assertEquals(3, verificationDataset.count());
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Assertions.assertEquals(3, verificationDataset.filter("type = 'other'").count());
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verificationDataset.show(false);
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//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright)
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}
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@Test
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public void testRecord() {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/singelRecord_pub.json")
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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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CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType());
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<CommunityResult> tmp = sc
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.textFile(workingDir.toString() + "/result")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
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Assertions.assertEquals(2, verificationDataset.count());
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verificationDataset.show(false);
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Assertions.assertEquals(2, verificationDataset.filter("type = 'publication'").count());
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}
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}
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