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@ -1,18 +1,12 @@
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package eu.dnetlib.dhp.oa.graph.clean;
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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 eu.dnetlib.dhp.oa.graph.dump.Constants;
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import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
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import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.dump.oaf.Instance;
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import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
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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.dhp.schema.oaf.StructuredProperty;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.util.List;
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import java.util.Locale;
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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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@ -27,133 +21,280 @@ 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 java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.util.List;
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import java.util.Locale;
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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 eu.dnetlib.dhp.oa.graph.dump.Constants;
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import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
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import eu.dnetlib.dhp.oa.graph.dump.DumpProducts;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.dump.oaf.Instance;
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import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute;
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import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult;
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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.dhp.schema.oaf.StructuredProperty;
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public class CleanContextTest {
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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(CleanContextTest.class);
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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 testResultClean() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json")
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.getPath();
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final String prefix = "gcube ";
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spark.read().textFile(sourcePath).map((MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class), Encoders.bean(Publication.class))
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.write().json(workingDir.toString() + "/publication");
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CleanContextSparkJob.main(new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--inputPath", workingDir.toString() + "/publication",
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"-graphTableClassName", Publication.class.getCanonicalName(),
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"-workingPath", workingDir.toString() + "/working",
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"-contextId","sobigdata",
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"-verifyParam","gCube "
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Publication> tmp = sc
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.textFile(workingDir.toString() + "/publication")
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.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
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Assertions.assertEquals(7, tmp.count());
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//original result with sobigdata context and gcube as starting string in the main title for the publication
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Assertions.assertEquals(0,
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tmp.filter(p->p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")).collect().get(0).getContext().size());
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//original result with sobigdata context without gcube as starting string in the main title for the publication
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Assertions.assertEquals(1,
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tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().size());
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Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).collect().get(0).getContext().get(0).getId() );
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//original result with sobigdata context with gcube as starting string in the subtitle
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Assertions.assertEquals(1,
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tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().size());
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Assertions.assertEquals("sobigdata::projects::2",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getContext().get(0).getId() );
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List<StructuredProperty> titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")).collect().get(0).getTitle();
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Assertions.assertEquals(1, titles.size());
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Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) );
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Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid());
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//original result with sobigdata context with gcube not as starting string in the main title
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Assertions.assertEquals(1,
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tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().size());
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Assertions.assertEquals("sobigdata::projects::1",tmp.filter(p->p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getContext().get(0).getId() );
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titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")).collect().get(0).getTitle();
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Assertions.assertEquals(1, titles.size());
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Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix) );
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Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()) );
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Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
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//original result with sobigdata in context and also other contexts with gcube as starting string for the main title
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Assertions.assertEquals(1,
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tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().size());
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Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getContext().get(0).getId() );
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titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")).collect().get(0).getTitle();
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Assertions.assertEquals(1, titles.size());
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Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix) );
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Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
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//original result with multiple main title one of which whith gcube as starting string and with 2 contextes
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Assertions.assertEquals(1,
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tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().size());
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Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getContext().get(0).getId() );
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titles = tmp.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")).collect().get(0).getTitle();
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Assertions.assertEquals(2, titles.size());
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Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)) );
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//original result without sobigdata in context with gcube as starting string for the main title
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Assertions.assertEquals(1,
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tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().size());
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Assertions.assertEquals("dh-ch",tmp.filter(p->p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getContext().get(0).getId() );
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titles = tmp.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")).collect().get(0).getTitle();
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Assertions.assertEquals(2, titles.size());
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Assertions.assertTrue(titles.stream().anyMatch(t -> t.getQualifier().getClassid().equals("main title") && t.getValue().toLowerCase().startsWith(prefix)));
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}
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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(CleanContextTest.class);
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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 testResultClean() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json")
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.getPath();
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final String prefix = "gcube ";
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spark
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.read()
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.textFile(sourcePath)
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.map(
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(MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class),
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Encoders.bean(Publication.class))
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.write()
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.json(workingDir.toString() + "/publication");
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CleanContextSparkJob.main(new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--inputPath", workingDir.toString() + "/publication",
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"-graphTableClassName", Publication.class.getCanonicalName(),
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"-workingPath", workingDir.toString() + "/working",
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"-contextId", "sobigdata",
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"-verifyParam", "gCube "
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Publication> tmp = sc
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.textFile(workingDir.toString() + "/publication")
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.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
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Assertions.assertEquals(7, tmp.count());
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// original result with sobigdata context and gcube as starting string in the main title for the publication
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Assertions
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.assertEquals(
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0,
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tmp
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.filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))
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.collect()
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.get(0)
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.getContext()
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.size());
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// original result with sobigdata context without gcube as starting string in the main title for the publication
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Assertions
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.assertEquals(
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1,
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tmp
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.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
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.collect()
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.get(0)
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.getContext()
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.size());
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Assertions
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.assertEquals(
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"sobigdata::projects::2",
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tmp
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.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
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.collect()
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.get(0)
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.getContext()
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.get(0)
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.getId());
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|
// original result with sobigdata context with gcube as starting string in the subtitle
|
|
|
|
|
Assertions
|
|
|
|
|
.assertEquals(
|
|
|
|
|
1,
|
|
|
|
|
tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getContext()
|
|
|
|
|
.size());
|
|
|
|
|
Assertions
|
|
|
|
|
.assertEquals(
|
|
|
|
|
"sobigdata::projects::2",
|
|
|
|
|
tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getContext()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getId());
|
|
|
|
|
List<StructuredProperty> titles = tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getTitle();
|
|
|
|
|
Assertions.assertEquals(1, titles.size());
|
|
|
|
|
Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix));
|
|
|
|
|
Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid());
|
|
|
|
|
|
|
|
|
|
// original result with sobigdata context with gcube not as starting string in the main title
|
|
|
|
|
Assertions
|
|
|
|
|
.assertEquals(
|
|
|
|
|
1,
|
|
|
|
|
tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getContext()
|
|
|
|
|
.size());
|
|
|
|
|
Assertions
|
|
|
|
|
.assertEquals(
|
|
|
|
|
"sobigdata::projects::1",
|
|
|
|
|
tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getContext()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getId());
|
|
|
|
|
titles = tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getTitle();
|
|
|
|
|
Assertions.assertEquals(1, titles.size());
|
|
|
|
|
Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix));
|
|
|
|
|
Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim()));
|
|
|
|
|
Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
|
|
|
|
|
|
|
|
|
|
// original result with sobigdata in context and also other contexts with gcube as starting string for the main
|
|
|
|
|
// title
|
|
|
|
|
Assertions
|
|
|
|
|
.assertEquals(
|
|
|
|
|
1,
|
|
|
|
|
tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getContext()
|
|
|
|
|
.size());
|
|
|
|
|
Assertions
|
|
|
|
|
.assertEquals(
|
|
|
|
|
"dh-ch",
|
|
|
|
|
tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getContext()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getId());
|
|
|
|
|
titles = tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getTitle();
|
|
|
|
|
Assertions.assertEquals(1, titles.size());
|
|
|
|
|
Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix));
|
|
|
|
|
Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid());
|
|
|
|
|
|
|
|
|
|
// original result with multiple main title one of which whith gcube as starting string and with 2 contextes
|
|
|
|
|
Assertions
|
|
|
|
|
.assertEquals(
|
|
|
|
|
1,
|
|
|
|
|
tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getContext()
|
|
|
|
|
.size());
|
|
|
|
|
Assertions
|
|
|
|
|
.assertEquals(
|
|
|
|
|
"dh-ch",
|
|
|
|
|
tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getContext()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getId());
|
|
|
|
|
titles = tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getTitle();
|
|
|
|
|
Assertions.assertEquals(2, titles.size());
|
|
|
|
|
Assertions
|
|
|
|
|
.assertTrue(
|
|
|
|
|
titles
|
|
|
|
|
.stream()
|
|
|
|
|
.anyMatch(
|
|
|
|
|
t -> t.getQualifier().getClassid().equals("main title")
|
|
|
|
|
&& t.getValue().toLowerCase().startsWith(prefix)));
|
|
|
|
|
|
|
|
|
|
// original result without sobigdata in context with gcube as starting string for the main title
|
|
|
|
|
Assertions
|
|
|
|
|
.assertEquals(
|
|
|
|
|
1,
|
|
|
|
|
tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getContext()
|
|
|
|
|
.size());
|
|
|
|
|
Assertions
|
|
|
|
|
.assertEquals(
|
|
|
|
|
"dh-ch",
|
|
|
|
|
tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getContext()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getId());
|
|
|
|
|
titles = tmp
|
|
|
|
|
.filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8"))
|
|
|
|
|
.collect()
|
|
|
|
|
.get(0)
|
|
|
|
|
.getTitle();
|
|
|
|
|
Assertions.assertEquals(2, titles.size());
|
|
|
|
|
|
|
|
|
|
Assertions
|
|
|
|
|
.assertTrue(
|
|
|
|
|
titles
|
|
|
|
|
.stream()
|
|
|
|
|
.anyMatch(
|
|
|
|
|
t -> t.getQualifier().getClassid().equals("main title")
|
|
|
|
|
&& t.getValue().toLowerCase().startsWith(prefix)));
|
|
|
|
|
|
|
|
|
|
}
|
|
|
|
|
}
|
|
|
|
|
|
