250 lines
12 KiB
Java
250 lines
12 KiB
Java
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package eu.dnetlib.dhp.bulktag;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.oaf.*;
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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.api.java.function.MapFunction;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.Row;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import 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 static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR;
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public class EOSCTagJobTest {
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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(EOSCTagJobTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(EOSCTagJobTest.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(EOSCTagJobTest.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(EOSCTagJobTest.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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void jupyterUpdatesTest() throws Exception {
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spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/software").getPath())
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.map((MapFunction<String, Software>) value -> OBJECT_MAPPER.readValue(value, Software.class), Encoders.bean(Software.class))
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.write()
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.option("compression","gzip")
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.json(workingDir.toString() + "/input/software");
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spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/dataset").getPath())
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.map((MapFunction<String, Dataset>) value -> OBJECT_MAPPER.readValue(value, Dataset.class), Encoders.bean(Dataset.class))
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.write()
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.option("compression","gzip")
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.json(workingDir.toString() + "/input/dataset");
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spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct").getPath())
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.map((MapFunction<String, OtherResearchProduct>) value -> OBJECT_MAPPER.readValue(value, OtherResearchProduct.class), Encoders.bean(OtherResearchProduct.class))
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.write()
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.option("compression","gzip")
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.json(workingDir.toString() + "/input/otherresearchproduct");
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SparkEoscTag
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath",
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workingDir.toString() + "/input",
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"-workingPath", workingDir.toString() + "/working"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Software> tmp = sc
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.textFile(workingDir.toString() + "/input/software")
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.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
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Assertions.assertEquals(10, tmp.count());
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Assertions.assertEquals(4, tmp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count());
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Assertions.assertEquals(2, tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect()
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.get(0).getSubject().size());
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Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect()
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.get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
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Assertions.assertEquals(5, tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect()
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.get(0).getSubject().size());
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Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect()
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.get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
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Assertions.assertEquals(9, tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect()
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.get(0).getSubject().size());
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Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect()
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.get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
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Assertions.assertEquals(5, tmp.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")).collect()
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.get(0).getSubject().size());
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Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")).collect()
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.get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
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Assertions.assertEquals(9, tmp.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")).collect()
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.get(0).getSubject().size());
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Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")).collect()
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.get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
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List<StructuredProperty> subjects = tmp.filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")).collect()
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.get(0).getSubject();
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Assertions.assertEquals(8, subjects.size());
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Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook")));
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Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("jupyter")));
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Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("Modeling and Simulation")));
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Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("structure granulaire")));
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Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("algorithme")));
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Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("simulation numérique")));
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Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de gaz")));
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Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de liquide")));
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Assertions.assertEquals(10, sc
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.textFile(workingDir.toString() + "/input/dataset")
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.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)).count());
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Assertions.assertEquals(0, sc
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.textFile(workingDir.toString() + "/input/dataset")
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.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)).filter(ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count());
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Assertions.assertEquals(10, sc
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.textFile(workingDir.toString() + "/input/otherresearchproduct")
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.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)).count());
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Assertions.assertEquals(0, sc
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.textFile(workingDir.toString() + "/input/otherresearchproduct")
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.map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)).filter(ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))).count());
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}
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@Test
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void galaxyUpdatesTest() throws Exception {
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spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/software").getPath())
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.map((MapFunction<String, Software>) value -> OBJECT_MAPPER.readValue(value, Software.class), Encoders.bean(Software.class))
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.write()
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.option("compression","gzip")
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.json(workingDir.toString() + "/input/software");
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spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/dataset").getPath())
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.map((MapFunction<String, Dataset>) value -> OBJECT_MAPPER.readValue(value, Dataset.class), Encoders.bean(Dataset.class))
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.write()
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.option("compression","gzip")
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.json(workingDir.toString() + "/input/dataset");
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spark.read().textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct").getPath())
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.map((MapFunction<String, OtherResearchProduct>) value -> OBJECT_MAPPER.readValue(value, OtherResearchProduct.class), Encoders.bean(OtherResearchProduct.class))
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.write()
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.option("compression","gzip")
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.json(workingDir.toString() + "/input/otherresearchproduct");
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SparkEoscTag
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-sourcePath",
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workingDir.toString() + "/input",
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"-workingPath", workingDir.toString() + "/working"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Software> tmp = sc
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.textFile(workingDir.toString() + "/input/software")
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.map(item -> OBJECT_MAPPER.readValue(item, Software.class));
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Assertions.assertEquals(10, tmp.count());
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Assertions.assertEquals(2, tmp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))).count());
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Assertions.assertEquals(2, tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect()
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.get(0).getSubject().size());
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Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")).collect()
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.get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
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Assertions.assertEquals(6, tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect()
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.get(0).getSubject().size());
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Assertions.assertTrue(tmp.filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")).collect()
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.get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
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Assertions.assertEquals(8, tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect()
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.get(0).getSubject().size());
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Assertions.assertFalse(tmp.filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")).collect()
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.get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
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JavaRDD<OtherResearchProduct> orp = sc.textFile(workingDir.toString() + "/input/otherresearchproduct").map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class));
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Assertions.assertEquals(10, orp.count());
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Assertions.assertEquals(2, orp.filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))).count());
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Assertions.assertEquals(3, orp.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")).collect()
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.get(0).getSubject().size());
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Assertions.assertTrue(orp.filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")).collect()
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.get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
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Assertions.assertEquals(2, orp.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")).collect()
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.get(0).getSubject().size());
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Assertions.assertFalse(orp.filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")).collect()
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.get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
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Assertions.assertEquals(3, orp.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")).collect()
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.get(0).getSubject().size());
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Assertions.assertTrue(orp.filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")).collect()
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.get(0).getSubject().stream().anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow")));
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}
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}
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