254 lines
9.0 KiB
Java
254 lines
9.0 KiB
Java
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package eu.dnetlib.dhp.bypassactionset;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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import static org.junit.jupiter.api.Assertions.assertTrue;
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import java.io.BufferedReader;
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import java.io.IOException;
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import java.io.InputStreamReader;
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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.stream.Collectors;
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import java.util.stream.Stream;
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import eu.dnetlib.dhp.PropagationConstant;
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import eu.dnetlib.dhp.bypassactionset.fos.SparkUpdateFOS;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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import org.apache.commons.io.FileUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.LocalFileSystem;
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import org.apache.neethi.Assertion;
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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.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.bypassactionset.fos.GetFOSData;
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import eu.dnetlib.dhp.bypassactionset.fos.PrepareFOSSparkJob;
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import eu.dnetlib.dhp.bypassactionset.model.FOSDataModel;
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import eu.dnetlib.dhp.common.collection.CollectorException;
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import eu.dnetlib.dhp.countrypropagation.CountryPropagationJobTest;
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import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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public class FOSTest {
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private static final Logger log = LoggerFactory.getLogger(FOSTest.class);
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private static Path workingDir;
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private static SparkSession spark;
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private static LocalFileSystem fs;
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final String ID_PREFIX = "50|doi_________";
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(CountryPropagationJobTest.class.getSimpleName());
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fs = FileSystem.getLocal(new Configuration());
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log.info("using work dir {}", workingDir);
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SparkConf conf = new SparkConf();
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conf.setAppName(FOSTest.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(CountryPropagationJobTest.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 getFOSFileTest() throws CollectorException, IOException, ClassNotFoundException {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/bypassactionset/fos/h2020_fos_sbs.csv")
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.getPath();
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final String outputPath = workingDir.toString() + "/fos.json";
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new GetFOSData()
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.doRewrite(sourcePath, outputPath, "eu.dnetlib.dhp.bypassactionset.FOSDataModel", '\t', fs);
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BufferedReader in = new BufferedReader(
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new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath))));
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String line;
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int count = 0;
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while ((line = in.readLine()) != null) {
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FOSDataModel fos = new ObjectMapper().readValue(line, FOSDataModel.class);
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System.out.println(new ObjectMapper().writeValueAsString(fos));
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count += 1;
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}
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assertEquals(38, count);
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}
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@Test
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void distributeDoiTest() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/bypassactionset/fos/fos.json")
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.getPath();
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PrepareFOSSparkJob
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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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"-outputPath", workingDir.toString() + "/distribute"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<FOSDataModel> tmp = sc
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.textFile(workingDir.toString() + "/distribute")
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.map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
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String doi1 = ID_PREFIX +
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IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.3390/s18072310"));
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assertEquals(50, tmp.count());
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assertEquals(1, tmp.filter(row -> row.getDoi().equals(doi1)).count());
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assertEquals(
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"engineering and technology", tmp.filter(r -> r.getDoi().equals(doi1)).collect().get(0).getLevel1());
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assertEquals("nano-technology", tmp.filter(r -> r.getDoi().equals(doi1)).collect().get(0).getLevel2());
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assertEquals(
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"nanoscience & nanotechnology", tmp.filter(r -> r.getDoi().equals(doi1)).collect().get(0).getLevel3());
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String doi = ID_PREFIX +
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IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/1365-2656.12831"));
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assertEquals(1, tmp.filter(row -> row.getDoi().equals(doi)).count());
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assertEquals("social sciences", tmp.filter(r -> r.getDoi().equals(doi)).collect().get(0).getLevel1());
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assertEquals(
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"psychology and cognitive sciences", tmp.filter(r -> r.getDoi().equals(doi)).collect().get(0).getLevel2());
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assertEquals("NULL", tmp.filter(r -> r.getDoi().equals(doi)).collect().get(0).getLevel3());
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}
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@Test
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void updateResult() throws Exception{
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final String fosPath = getClass()
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.getResource("/eu/dnetlib/dhp/bypassactionset/fos/fos_prepared.json")
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.getPath();
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final String inputPath = getClass()
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.getResource("/eu/dnetlib/dhp/bypassactionset/bip/publicationnomatch.json")
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.getPath();
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SparkUpdateFOS
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.main(
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new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--fosPath", fosPath,
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"--inputPath", inputPath,
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"--outputPath", workingDir.toString() + "/publication",
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"--resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication"
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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(6, tmp.count());
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tmp.filter(r -> r.getSubject() != null).map(p -> p.getSubject())
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.foreach(s -> s.stream().forEach(sbj -> Assertions.assertFalse("FOS".equals(sbj.getQualifier().getClassid()))));
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}
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@Test
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void updateResultMatch() throws Exception{
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final String fosPath = getClass()
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.getResource("/eu/dnetlib/dhp/bypassactionset/fos/fos_prepared.json")
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.getPath();
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final String inputPath = getClass()
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.getResource("/eu/dnetlib/dhp/bypassactionset/fos/publicationmatch.json")
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.getPath();
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SparkUpdateFOS
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.main(
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new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--fosPath", fosPath,
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"--inputPath", inputPath,
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"--outputPath", workingDir.toString() + "/publication",
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"--resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication"
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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(6, tmp.count());
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Assertions.assertEquals(3, tmp.filter(r -> r.getSubject() != null).map(p -> p.getSubject()).flatMap(v -> v.iterator())
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.filter(sbj -> sbj.getQualifier().getClassid().equals("FOS")).collect().size());
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List<StructuredProperty> sbjs = tmp.filter(r -> r.getId().equals("50|doi_________b24ab3e127aa67e2a1017292988d571f"))
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.map(p -> p.getSubject()).collect().get(0);
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Assertions.assertEquals(12, sbjs.size());
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Stream<StructuredProperty> fosSubjs = sbjs.stream().filter(sbj -> sbj.getQualifier().getClassid().equals("FOS"));
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Assertions.assertTrue(fosSubjs
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.map(sbj -> sbj.getValue()).collect(Collectors.toList()).contains("engineering and technology"));
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Assertions.assertTrue(fosSubjs
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.map(sbj -> sbj.getValue()).collect(Collectors.toList()).contains("nano-technology"));
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Assertions.assertTrue(fosSubjs
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.map(sbj -> sbj.getValue()).collect(Collectors.toList()).contains("nanoscience & nanotechnology"));
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fosSubjs.forEach(sbj -> Assertions.assertEquals("update", sbj.getDataInfo().getInferenceprovenance()) );
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fosSubjs.forEach(sbj -> Assertions.assertEquals("subject:fos", sbj.getDataInfo().getProvenanceaction().getClassid()) );
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fosSubjs.forEach(sbj -> Assertions.assertEquals("Inferred by OpenAIRE", sbj.getDataInfo().getProvenanceaction().getClassname() ));
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fosSubjs.forEach(sbj -> Assertions.assertEquals("", sbj.getDataInfo().getTrust() ));
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fosSubjs.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getDeletedbyinference() ));
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fosSubjs.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getInvisible() ));
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fosSubjs.forEach(sbj -> Assertions.assertEquals(true, sbj.getDataInfo().getInferred() ));
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}
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}
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