forked from D-Net/dnet-hadoop
job test for class producing first step of results dump
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package eu.dnetlib.dhp.oa.graph.dump;
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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.raw.common.VocabularyGroup;
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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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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException;
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import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
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import org.apache.commons.io.FileUtils;
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import org.apache.commons.io.IOUtils;
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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.dom4j.DocumentException;
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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 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.HashMap;
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import java.util.List;
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import org.junit.jupiter.api.extension.ExtendWith;
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import org.mockito.Mock;
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import org.mockito.junit.jupiter.MockitoExtension;
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import static org.mockito.Mockito.lenient;
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import static org.mockito.Mockito.when;
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@ExtendWith(MockitoExtension.class)
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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 String MOCK_IS_LOOK_UP_URL = "https://beta.services.openaire.eu/is/services/isLookUp";
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private static final Logger log = LoggerFactory.getLogger(DumpJobTest.class);
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private static HashMap<String,String> map = new HashMap<>();
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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");map.put("fam", "Fisheries and Aquaculture Management");map.put("ni", "Neuroinformatics");map.put("mes", "European Marine Scinece");map.put("instruct", "Instruct-Eric");
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map.put("rda", "Research Data Alliance");map.put("elixir-gr", "ELIXIR GR");map.put("aginfra", "Agricultural and Food Sciences");map.put("dariah", "DARIAH EU");map.put("risis", "RISI");
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map.put("ee", "SDSN - Greece");map.put("oa-pg", "EC Post-Grant Open Access Pilot");map.put("beopen", "Transport Research");map.put("euromarine", "Euromarine");map.put("ifremer", "Ifremer");
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map.put("dh-ch", "Digital Humanities and Cultural Heritage");map.put("science-innovation-policy", "Science and Innovation Policy Studies");map.put("covid-19", "COVID-19");map.put("enrmaps", "Energy Research");map.put("epos", "EPOS");
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}
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List<String> communityMap = Arrays.asList("<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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@Mock
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private SparkDumpCommunityProducts dumpCommunityProducts;
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private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " +
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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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@BeforeEach
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public void setUp() throws ISLookUpException {
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lenient().when(dumpCommunityProducts.getCommunityMap(MOCK_IS_LOOK_UP_URL)).thenReturn(map);
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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 test1() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/dataset.json")
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.getPath();
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dumpCommunityProducts
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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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"-resultType","dataset",
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
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"-dumpTableName","eu.dnetlib.dhp.schema.dump.oaf.Dataset",
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"-outputPath", workingDir.toString() + "/dataset",
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"-isLookUpUrl", MOCK_IS_LOOK_UP_URL
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<eu.dnetlib.dhp.schema.dump.oaf.Dataset> tmp = sc
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.textFile(workingDir.toString() + "/dataset")
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.map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.dump.oaf.Dataset.class));
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org.apache.spark.sql.Dataset<eu.dnetlib.dhp.schema.dump.oaf.Dataset> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.Dataset.class));
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verificationDataset.show(false);
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}
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// @Test
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// public void bulktagBySubjectNoPreviousContextTest() throws Exception {
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// final String sourcePath = getClass()
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// .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/nocontext")
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// .getPath();
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// final String pathMap = DumpJobTest.pathMap;
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// DumpJobTest
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// .main(
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// new String[] {
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// "-isTest", Boolean.TRUE.toString(),
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// "-isSparkSessionManaged", Boolean.FALSE.toString(),
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// "-sourcePath", sourcePath,
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// "-taggingConf", taggingConf,
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// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
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// "-outputPath", workingDir.toString() + "/dataset",
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// "-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
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// "-pathMap", pathMap
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// });
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//
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// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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//
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// JavaRDD<Dataset> tmp = sc
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// .textFile(workingDir.toString() + "/dataset")
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// .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
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//
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// Assertions.assertEquals(10, tmp.count());
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// org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
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// .createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
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//
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// verificationDataset.createOrReplaceTempView("dataset");
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//
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// String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
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// + "from dataset "
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// + "lateral view explode(context) c as MyT "
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// + "lateral view explode(MyT.datainfo) d as MyD "
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// + "where MyD.inferenceprovenance = 'bulktagging'";
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//
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// Assertions.assertEquals(5, spark.sql(query).count());
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//
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// org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
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// Assertions
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// .assertEquals(
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// 5, idExplodeCommunity.filter("provenance = 'community:subject'").count());
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// Assertions
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// .assertEquals(
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// 5,
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// idExplodeCommunity.filter("name = 'Bulktagging for Community - Subject'").count());
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//
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// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count());
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// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count());
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// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count());
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// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count());
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//
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// Assertions
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// .assertEquals(
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// 1,
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// idExplodeCommunity
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// .filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'")
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// .count());
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// Assertions
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// .assertEquals(
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// 1,
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// idExplodeCommunity
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// .filter(
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// "community = 'covid-19' and id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'")
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// .count());
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//
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// Assertions
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// .assertEquals(
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// 2,
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// idExplodeCommunity
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// .filter("id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'")
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// .count());
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// Assertions
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// .assertEquals(
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// 2,
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// idExplodeCommunity
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// .filter(
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// "(community = 'covid-19' or community = 'aginfra') and id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b'")
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// .count());
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//
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// Assertions
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// .assertEquals(
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// 2,
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// idExplodeCommunity
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// .filter("id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'")
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// .count());
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// Assertions
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// .assertEquals(
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// 2,
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// idExplodeCommunity
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// .filter(
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// "(community = 'mes' or community = 'fam') and id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62'")
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// .count());
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// }
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//
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// @Test
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// public void bulktagBySubjectPreviousContextNoProvenanceTest() throws Exception {
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// final String sourcePath = getClass()
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// .getResource(
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// "/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject/contextnoprovenance")
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// .getPath();
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// final String pathMap = BulkTagJobTest.pathMap;
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// SparkBulkTagJob
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// .main(
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// new String[] {
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// "-isTest", Boolean.TRUE.toString(),
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// "-isSparkSessionManaged", Boolean.FALSE.toString(),
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// "-sourcePath", sourcePath,
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// "-taggingConf", taggingConf,
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// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
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// "-outputPath", workingDir.toString() + "/dataset",
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// "-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
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// "-pathMap", pathMap
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// });
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//
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// final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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//
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// JavaRDD<Dataset> tmp = sc
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// .textFile(workingDir.toString() + "/dataset")
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// .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
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//
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// Assertions.assertEquals(10, tmp.count());
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// org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
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// .createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
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//
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// verificationDataset.createOrReplaceTempView("dataset");
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//
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// String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance "
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// + "from dataset "
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// + "lateral view explode(context) c as MyT "
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// + "lateral view explode(MyT.datainfo) d as MyD "
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// + "where MyT.id = 'covid-19' ";
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//
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// Assertions.assertEquals(3, spark.sql(query).count());
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//
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// org.apache.spark.sql.Dataset<Row> communityContext = spark.sql(query);
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//
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// Assertions
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// .assertEquals(
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// 2,
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// communityContext
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// .filter("id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529'")
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// .count());
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// Assertions
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// .assertEquals(
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// 1,
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// communityContext
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// .filter(
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// "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'community:subject'")
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// .count());
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// Assertions
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// .assertEquals(
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// 1,
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// communityContext
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// .filter(
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// "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and provenance = 'propagation:community:productsthroughsemrel'")
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// .count());
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//
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// query = "select id, MyT.id community, size(MyT.datainfo) datainfosize "
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// + "from dataset "
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// + "lateral view explode (context) as MyT "
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// + "where size(MyT.datainfo) > 0";
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//
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// Assertions
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// .assertEquals(
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// 2,
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// spark
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|
// .sql(query)
|
||||||
|
// .select("datainfosize")
|
||||||
|
// .where(
|
||||||
|
// "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' a"
|
||||||
|
// + "nd community = 'covid-19'")
|
||||||
|
// .collectAsList()
|
||||||
|
// .get(0)
|
||||||
|
// .getInt(0));
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// @Test
|
||||||
|
// public void bulktagByDatasourceTest() throws Exception {
|
||||||
|
// final String sourcePath = getClass()
|
||||||
|
// .getResource("/eu/dnetlib/dhp/bulktag/sample/publication/update_datasource")
|
||||||
|
// .getPath();
|
||||||
|
// SparkBulkTagJob
|
||||||
|
// .main(
|
||||||
|
// new String[] {
|
||||||
|
// "-isTest", Boolean.TRUE.toString(),
|
||||||
|
// "-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
|
// "-sourcePath", sourcePath,
|
||||||
|
// "-taggingConf", taggingConf,
|
||||||
|
// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
|
||||||
|
// "-outputPath", workingDir.toString() + "/publication",
|
||||||
|
// "-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
||||||
|
// "-pathMap", pathMap
|
||||||
|
// });
|
||||||
|
//
|
||||||
|
// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||||
|
//
|
||||||
|
// JavaRDD<Publication> tmp = sc
|
||||||
|
// .textFile(workingDir.toString() + "/publication")
|
||||||
|
// .map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
|
||||||
|
//
|
||||||
|
// Assertions.assertEquals(10, tmp.count());
|
||||||
|
// org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
|
||||||
|
// .createDataset(tmp.rdd(), Encoders.bean(Publication.class));
|
||||||
|
//
|
||||||
|
// verificationDataset.createOrReplaceTempView("publication");
|
||||||
|
//
|
||||||
|
// String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
|
||||||
|
// + "from publication "
|
||||||
|
// + "lateral view explode(context) c as MyT "
|
||||||
|
// + "lateral view explode(MyT.datainfo) d as MyD "
|
||||||
|
// + "where MyD.inferenceprovenance = 'bulktagging'";
|
||||||
|
//
|
||||||
|
// org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
|
||||||
|
//
|
||||||
|
// Assertions.assertEquals(5, idExplodeCommunity.count());
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 5, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 5,
|
||||||
|
// idExplodeCommunity
|
||||||
|
// .filter("name = 'Bulktagging for Community - Datasource'")
|
||||||
|
// .count());
|
||||||
|
//
|
||||||
|
// Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'fam'").count());
|
||||||
|
// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count());
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 3,
|
||||||
|
// idExplodeCommunity
|
||||||
|
// .filter(
|
||||||
|
// "community = 'fam' and (id = '50|ec_fp7health::000085c89f4b96dc2269bd37edb35306' "
|
||||||
|
// + "or id = '50|ec_fp7health::000b9e61f83f5a4b0c35777b7bccdf38' "
|
||||||
|
// + "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')")
|
||||||
|
// .count());
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 2,
|
||||||
|
// idExplodeCommunity
|
||||||
|
// .filter(
|
||||||
|
// "community = 'aginfra' and (id = '50|ec_fp7health::000c8195edd542e4e64ebb32172cbf89' "
|
||||||
|
// + "or id = '50|ec_fp7health::0010eb63e181e3e91b8b6dc6b3e1c798')")
|
||||||
|
// .count());
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// @Test
|
||||||
|
// public void bulktagByZenodoCommunityTest() throws Exception {
|
||||||
|
// final String sourcePath = getClass()
|
||||||
|
// .getResource(
|
||||||
|
// "/eu/dnetlib/dhp/bulktag/sample/otherresearchproduct/update_zenodocommunity")
|
||||||
|
// .getPath();
|
||||||
|
// SparkBulkTagJob
|
||||||
|
// .main(
|
||||||
|
// new String[] {
|
||||||
|
// "-isTest", Boolean.TRUE.toString(),
|
||||||
|
// "-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
|
// "-sourcePath", sourcePath,
|
||||||
|
// "-taggingConf", taggingConf,
|
||||||
|
// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.OtherResearchProduct",
|
||||||
|
// "-outputPath", workingDir.toString() + "/orp",
|
||||||
|
// "-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
||||||
|
// "-pathMap", pathMap
|
||||||
|
// });
|
||||||
|
//
|
||||||
|
// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||||
|
//
|
||||||
|
// JavaRDD<OtherResearchProduct> tmp = sc
|
||||||
|
// .textFile(workingDir.toString() + "/orp")
|
||||||
|
// .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
|
||||||
|
//
|
||||||
|
// Assertions.assertEquals(10, tmp.count());
|
||||||
|
// org.apache.spark.sql.Dataset<OtherResearchProduct> verificationDataset = spark
|
||||||
|
// .createDataset(tmp.rdd(), Encoders.bean(OtherResearchProduct.class));
|
||||||
|
//
|
||||||
|
// verificationDataset.createOrReplaceTempView("orp");
|
||||||
|
//
|
||||||
|
// String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
|
||||||
|
// + "from orp "
|
||||||
|
// + "lateral view explode(context) c as MyT "
|
||||||
|
// + "lateral view explode(MyT.datainfo) d as MyD "
|
||||||
|
// + "where MyD.inferenceprovenance = 'bulktagging'";
|
||||||
|
//
|
||||||
|
// org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
|
||||||
|
// Assertions.assertEquals(8, idExplodeCommunity.count());
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 8, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count());
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 8,
|
||||||
|
// idExplodeCommunity.filter("name = 'Bulktagging for Community - Zenodo'").count());
|
||||||
|
//
|
||||||
|
// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'covid-19'").count());
|
||||||
|
// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'aginfra'").count());
|
||||||
|
// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'beopen'").count());
|
||||||
|
// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count());
|
||||||
|
// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'mes'").count());
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 1,
|
||||||
|
// idExplodeCommunity
|
||||||
|
// .filter(
|
||||||
|
// "id = '50|od______2017::0750a4d0782265873d669520f5e33c07' "
|
||||||
|
// + "and community = 'covid-19'")
|
||||||
|
// .count());
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 3,
|
||||||
|
// idExplodeCommunity
|
||||||
|
// .filter(
|
||||||
|
// "id = '50|od______2017::1bd97baef19dbd2db3203b112bb83bc5' and "
|
||||||
|
// + "(community = 'aginfra' or community = 'mes' or community = 'fam')")
|
||||||
|
// .count());
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 1,
|
||||||
|
// idExplodeCommunity
|
||||||
|
// .filter(
|
||||||
|
// "id = '50|od______2017::1e400f1747487fd15998735c41a55c72' "
|
||||||
|
// + "and community = 'beopen'")
|
||||||
|
// .count());
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 3,
|
||||||
|
// idExplodeCommunity
|
||||||
|
// .filter(
|
||||||
|
// "id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' and "
|
||||||
|
// + "(community = 'beopen' or community = 'fam' or community = 'mes')")
|
||||||
|
// .count());
|
||||||
|
//
|
||||||
|
// query = "select id, MyT.id community, size(MyT.datainfo) datainfosize "
|
||||||
|
// + "from orp "
|
||||||
|
// + "lateral view explode (context) as MyT "
|
||||||
|
// + "where size(MyT.datainfo) > 0";
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 2,
|
||||||
|
// spark
|
||||||
|
// .sql(query)
|
||||||
|
// .select("datainfosize")
|
||||||
|
// .where(
|
||||||
|
// "id = '50|od______2017::210281c5bc1c739a11ccceeeca806396' a"
|
||||||
|
// + "nd community = 'beopen'")
|
||||||
|
// .collectAsList()
|
||||||
|
// .get(0)
|
||||||
|
// .getInt(0));
|
||||||
|
//
|
||||||
|
// // verify the zenodo community context is not present anymore in the records
|
||||||
|
// query = "select id, MyT.id community "
|
||||||
|
// + "from orp "
|
||||||
|
// + "lateral view explode(context) c as MyT "
|
||||||
|
// + "lateral view explode(MyT.datainfo) d as MyD ";
|
||||||
|
//
|
||||||
|
// org.apache.spark.sql.Dataset<Row> tmp2 = spark.sql(query);
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 0,
|
||||||
|
// tmp2
|
||||||
|
// .select("community")
|
||||||
|
// .where(tmp2.col("community").contains(ZENODO_COMMUNITY_INDICATOR))
|
||||||
|
// .count());
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// @Test
|
||||||
|
// public void bulktagBySubjectDatasourceTest() throws Exception {
|
||||||
|
// final String sourcePath = getClass()
|
||||||
|
// .getResource("/eu/dnetlib/dhp/bulktag/sample/dataset/update_subject_datasource")
|
||||||
|
// .getPath();
|
||||||
|
// SparkBulkTagJob
|
||||||
|
// .main(
|
||||||
|
// new String[] {
|
||||||
|
// "-isTest", Boolean.TRUE.toString(),
|
||||||
|
// "-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
|
// "-sourcePath", sourcePath,
|
||||||
|
// "-taggingConf", taggingConf,
|
||||||
|
// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
||||||
|
// "-outputPath", workingDir.toString() + "/dataset",
|
||||||
|
// "-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
||||||
|
// "-pathMap", pathMap
|
||||||
|
// });
|
||||||
|
//
|
||||||
|
// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||||
|
//
|
||||||
|
// JavaRDD<Dataset> tmp = sc
|
||||||
|
// .textFile(workingDir.toString() + "/dataset")
|
||||||
|
// .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
||||||
|
//
|
||||||
|
// Assertions.assertEquals(10, tmp.count());
|
||||||
|
// org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
|
||||||
|
// .createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
|
||||||
|
//
|
||||||
|
// verificationDataset.createOrReplaceTempView("dataset");
|
||||||
|
//
|
||||||
|
// String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
|
||||||
|
// + "from dataset "
|
||||||
|
// + "lateral view explode(context) c as MyT "
|
||||||
|
// + "lateral view explode(MyT.datainfo) d as MyD "
|
||||||
|
// + "where MyD.inferenceprovenance = 'bulktagging'";
|
||||||
|
//
|
||||||
|
// org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
|
||||||
|
// Assertions.assertEquals(7, idExplodeCommunity.count());
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 5, idExplodeCommunity.filter("provenance = 'community:subject'").count());
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 2, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
|
||||||
|
// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'covid-19'").count());
|
||||||
|
// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'fam'").count());
|
||||||
|
// Assertions.assertEquals(2, idExplodeCommunity.filter("community = 'aginfra'").count());
|
||||||
|
// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'mes'").count());
|
||||||
|
//
|
||||||
|
// query = "select id, MyT.id community, size(MyT.datainfo) datainfosize "
|
||||||
|
// + "from dataset "
|
||||||
|
// + "lateral view explode (context) as MyT "
|
||||||
|
// + "where size(MyT.datainfo) > 0";
|
||||||
|
//
|
||||||
|
// org.apache.spark.sql.Dataset<Row> tmp2 = spark.sql(query);
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 2,
|
||||||
|
// tmp2
|
||||||
|
// .select("datainfosize")
|
||||||
|
// .where(
|
||||||
|
// "id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and "
|
||||||
|
// + "community = 'aginfra'")
|
||||||
|
// .collectAsList()
|
||||||
|
// .get(0)
|
||||||
|
// .getInt(0));
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 1,
|
||||||
|
// tmp2
|
||||||
|
// .select("datainfosize")
|
||||||
|
// .where(
|
||||||
|
// "id = '50|od______3989::05d8c751462f9bb8d2b06956dfbc5c7b' and "
|
||||||
|
// + "community = 'covid-19'")
|
||||||
|
// .collectAsList()
|
||||||
|
// .get(0)
|
||||||
|
// .getInt(0));
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 2,
|
||||||
|
// tmp2
|
||||||
|
// .select("datainfosize")
|
||||||
|
// .where(
|
||||||
|
// "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and "
|
||||||
|
// + "community = 'fam'")
|
||||||
|
// .collectAsList()
|
||||||
|
// .get(0)
|
||||||
|
// .getInt(0));
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 2,
|
||||||
|
// tmp2
|
||||||
|
// .select("datainfosize")
|
||||||
|
// .where(
|
||||||
|
// "id = '50|od______3989::02dd5d2c222191b0b9bd4f33c8e96529' and "
|
||||||
|
// + "community = 'covid-19'")
|
||||||
|
// .collectAsList()
|
||||||
|
// .get(0)
|
||||||
|
// .getInt(0));
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 1,
|
||||||
|
// tmp2
|
||||||
|
// .select("datainfosize")
|
||||||
|
// .where(
|
||||||
|
// "id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and "
|
||||||
|
// + "community = 'fam'")
|
||||||
|
// .collectAsList()
|
||||||
|
// .get(0)
|
||||||
|
// .getInt(0));
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 1,
|
||||||
|
// tmp2
|
||||||
|
// .select("datainfosize")
|
||||||
|
// .where(
|
||||||
|
// "id = '50|od______3989::0f89464c4ac4c398fe0c71433b175a62' and "
|
||||||
|
// + "community = 'mes'")
|
||||||
|
// .collectAsList()
|
||||||
|
// .get(0)
|
||||||
|
// .getInt(0));
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// @Test
|
||||||
|
// public void bulktagBySubjectDatasourceZenodoCommunityTest() throws Exception {
|
||||||
|
//
|
||||||
|
// SparkBulkTagJob
|
||||||
|
// .main(
|
||||||
|
// new String[] {
|
||||||
|
// "-isTest", Boolean.TRUE.toString(),
|
||||||
|
// "-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
|
// "-sourcePath", getClass().getResource("/eu/dnetlib/dhp/bulktag/sample/software/").getPath(),
|
||||||
|
// "-taggingConf", taggingConf,
|
||||||
|
// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Software",
|
||||||
|
// "-outputPath", workingDir.toString() + "/software",
|
||||||
|
// "-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
||||||
|
// "-pathMap", pathMap
|
||||||
|
// });
|
||||||
|
//
|
||||||
|
// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||||
|
//
|
||||||
|
// JavaRDD<Software> tmp = sc
|
||||||
|
// .textFile(workingDir.toString() + "/software")
|
||||||
|
// .map(item -> OBJECT_MAPPER.readValue(item, Software.class));
|
||||||
|
//
|
||||||
|
// Assertions.assertEquals(10, tmp.count());
|
||||||
|
// org.apache.spark.sql.Dataset<Software> verificationDataset = spark
|
||||||
|
// .createDataset(tmp.rdd(), Encoders.bean(Software.class));
|
||||||
|
//
|
||||||
|
// verificationDataset.createOrReplaceTempView("software");
|
||||||
|
//
|
||||||
|
// String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
|
||||||
|
// + "from software "
|
||||||
|
// + "lateral view explode(context) c as MyT "
|
||||||
|
// + "lateral view explode(MyT.datainfo) d as MyD "
|
||||||
|
// + "where MyD.inferenceprovenance = 'bulktagging'";
|
||||||
|
//
|
||||||
|
// org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
|
||||||
|
// Assertions.assertEquals(10, idExplodeCommunity.count());
|
||||||
|
//
|
||||||
|
// idExplodeCommunity.show(false);
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 3, idExplodeCommunity.filter("provenance = 'community:subject'").count());
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 4, idExplodeCommunity.filter("provenance = 'community:zenodocommunity'").count());
|
||||||
|
//
|
||||||
|
// Assertions.assertEquals(3, idExplodeCommunity.filter("community = 'covid-19'").count());
|
||||||
|
// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dh-ch'").count());
|
||||||
|
// Assertions.assertEquals(4, idExplodeCommunity.filter("community = 'aginfra'").count());
|
||||||
|
// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'dariah'").count());
|
||||||
|
// Assertions.assertEquals(1, idExplodeCommunity.filter("community = 'fam'").count());
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 2,
|
||||||
|
// idExplodeCommunity
|
||||||
|
// .filter(
|
||||||
|
// "provenance = 'community:zenodocommunity' and "
|
||||||
|
// + "id = '50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4' and ("
|
||||||
|
// + "community = 'dh-ch' or community = 'dariah')")
|
||||||
|
// .count());
|
||||||
|
//
|
||||||
|
// query = "select id, MyT.id community, size(MyT.datainfo) datainfosize "
|
||||||
|
// + "from software "
|
||||||
|
// + "lateral view explode (context) as MyT "
|
||||||
|
// + "where size(MyT.datainfo) > 0";
|
||||||
|
//
|
||||||
|
// org.apache.spark.sql.Dataset<Row> tmp2 = spark.sql(query);
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 2,
|
||||||
|
// tmp2
|
||||||
|
// .select("datainfosize")
|
||||||
|
// .where(
|
||||||
|
// "id = '50|od______1582::501b25d420f808c8eddcd9b16e917f11' and "
|
||||||
|
// + "community = 'covid-19'")
|
||||||
|
// .collectAsList()
|
||||||
|
// .get(0)
|
||||||
|
// .getInt(0));
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 3,
|
||||||
|
// tmp2
|
||||||
|
// .select("datainfosize")
|
||||||
|
// .where(
|
||||||
|
// "id = '50|od______1582::581621232a561b7e8b4952b18b8b0e56' and "
|
||||||
|
// + "community = 'aginfra'")
|
||||||
|
// .collectAsList()
|
||||||
|
// .get(0)
|
||||||
|
// .getInt(0));
|
||||||
|
// }
|
||||||
|
//
|
||||||
|
// @Test
|
||||||
|
// public void bulktagDatasourcewithConstraintsTest() throws Exception {
|
||||||
|
//
|
||||||
|
// final String sourcePath = getClass()
|
||||||
|
// .getResource(
|
||||||
|
// "/eu/dnetlib/dhp/bulktag/sample/dataset/update_datasourcewithconstraints")
|
||||||
|
// .getPath();
|
||||||
|
// SparkBulkTagJob
|
||||||
|
// .main(
|
||||||
|
// new String[] {
|
||||||
|
// "-isTest", Boolean.TRUE.toString(),
|
||||||
|
// "-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
|
// "-sourcePath", sourcePath,
|
||||||
|
// "-taggingConf", taggingConf,
|
||||||
|
// "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
||||||
|
// "-outputPath", workingDir.toString() + "/dataset",
|
||||||
|
// "-isLookUpUrl", MOCK_IS_LOOK_UP_URL,
|
||||||
|
// "-pathMap", pathMap
|
||||||
|
// });
|
||||||
|
//
|
||||||
|
// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||||
|
//
|
||||||
|
// JavaRDD<Dataset> tmp = sc
|
||||||
|
// .textFile(workingDir.toString() + "/dataset")
|
||||||
|
// .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
||||||
|
//
|
||||||
|
// Assertions.assertEquals(10, tmp.count());
|
||||||
|
// org.apache.spark.sql.Dataset<Dataset> verificationDataset = spark
|
||||||
|
// .createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
|
||||||
|
//
|
||||||
|
// verificationDataset.createOrReplaceTempView("dataset");
|
||||||
|
// String query = "select id, MyT.id community, MyD.provenanceaction.classid provenance, MyD.provenanceaction.classname name "
|
||||||
|
// + "from dataset "
|
||||||
|
// + "lateral view explode(context) c as MyT "
|
||||||
|
// + "lateral view explode(MyT.datainfo) d as MyD "
|
||||||
|
// + "where MyD.inferenceprovenance = 'bulktagging'";
|
||||||
|
//
|
||||||
|
// org.apache.spark.sql.Dataset<Row> idExplodeCommunity = spark.sql(query);
|
||||||
|
//
|
||||||
|
// idExplodeCommunity.show(false);
|
||||||
|
// Assertions.assertEquals(3, idExplodeCommunity.count());
|
||||||
|
//
|
||||||
|
// Assertions
|
||||||
|
// .assertEquals(
|
||||||
|
// 3, idExplodeCommunity.filter("provenance = 'community:datasource'").count());
|
||||||
|
// }
|
||||||
|
}
|
||||||
File diff suppressed because one or more lines are too long
Loading…
Reference in New Issue