forked from D-Net/dnet-hadoop
584 lines
17 KiB
Java
584 lines
17 KiB
Java
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package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
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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.stream.Collectors;
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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.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.actionmanager.Constants;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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public class ProduceTest {
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private static final Logger log = LoggerFactory.getLogger(ProduceTest.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(ProduceTest.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(ProduceTest.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(ProduceTest.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 produceTestSubjects() throws Exception {
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JavaRDD<Result> tmp = getResultJavaRDD();
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List<StructuredProperty> sbjs = tmp
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.filter(row -> row.getSubject() != null && row.getSubject().size() > 0)
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.flatMap(row -> row.getSubject().iterator())
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.collect();
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sbjs.forEach(sbj -> Assertions.assertEquals("FOS", sbj.getQualifier().getClassid()));
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sbjs
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.forEach(
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sbj -> Assertions
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.assertEquals(
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"Fields of Science and Technology classification", sbj.getQualifier().getClassname()));
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sbjs
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.forEach(
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sbj -> Assertions
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.assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemeid()));
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sbjs
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.forEach(
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sbj -> Assertions
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.assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemename()));
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sbjs.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getDeletedbyinference()));
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sbjs.forEach(sbj -> Assertions.assertEquals(true, sbj.getDataInfo().getInferred()));
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sbjs.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getInvisible()));
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sbjs.forEach(sbj -> Assertions.assertEquals("", sbj.getDataInfo().getTrust()));
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sbjs.forEach(sbj -> Assertions.assertEquals("update", sbj.getDataInfo().getInferenceprovenance()));
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sbjs
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.forEach(
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sbj -> Assertions.assertEquals("subject:fos", sbj.getDataInfo().getProvenanceaction().getClassid()));
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sbjs
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.forEach(
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sbj -> Assertions
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.assertEquals("Inferred by OpenAIRE", sbj.getDataInfo().getProvenanceaction().getClassname()));
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sbjs
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.forEach(
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sbj -> Assertions
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.assertEquals(
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ModelConstants.DNET_PROVENANCE_ACTIONS, sbj.getDataInfo().getProvenanceaction().getSchemeid()));
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sbjs
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.forEach(
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sbj -> Assertions
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.assertEquals(
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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sbj.getDataInfo().getProvenanceaction().getSchemename()));
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}
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@Test
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void produceTestMeasuress() throws Exception {
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JavaRDD<Result> tmp = getResultJavaRDD();
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List<KeyValue> mes = tmp
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.filter(row -> row.getInstance() != null && row.getInstance().size() > 0)
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.flatMap(row -> row.getInstance().iterator())
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.flatMap(i -> i.getMeasures().iterator())
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.flatMap(m -> m.getUnit().iterator())
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.collect();
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mes.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getDeletedbyinference()));
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mes.forEach(sbj -> Assertions.assertEquals(true, sbj.getDataInfo().getInferred()));
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mes.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getInvisible()));
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mes.forEach(sbj -> Assertions.assertEquals("", sbj.getDataInfo().getTrust()));
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mes.forEach(sbj -> Assertions.assertEquals("update", sbj.getDataInfo().getInferenceprovenance()));
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mes
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.forEach(
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sbj -> Assertions.assertEquals("measure:bip", sbj.getDataInfo().getProvenanceaction().getClassid()));
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mes
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.forEach(
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sbj -> Assertions
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.assertEquals("Inferred by OpenAIRE", sbj.getDataInfo().getProvenanceaction().getClassname()));
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mes
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.forEach(
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sbj -> Assertions
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.assertEquals(
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ModelConstants.DNET_PROVENANCE_ACTIONS, sbj.getDataInfo().getProvenanceaction().getSchemeid()));
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mes
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.forEach(
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sbj -> Assertions
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.assertEquals(
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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sbj.getDataInfo().getProvenanceaction().getSchemename()));
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}
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@Test
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void produceTest6Subjects() throws Exception {
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final String doi = "unresolved::10.3390/s18072310::doi";
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JavaRDD<Result> tmp = getResultJavaRDD();
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Assertions
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.assertEquals(
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6, tmp
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.filter(row -> row.getId().equals(doi))
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.collect()
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.get(0)
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.getSubject()
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.size());
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List<StructuredProperty> sbjs = tmp
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.filter(row -> row.getId().equals(doi))
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.flatMap(row -> row.getSubject().iterator())
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.collect();
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Assertions
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.assertEquals(
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true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("04 agricultural and veterinary sciences")));
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Assertions
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.assertEquals(
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true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0404 agricultural biotechnology")));
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Assertions.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("040502 food science")));
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Assertions
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.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("03 medical and health sciences")));
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Assertions.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0303 health sciences")));
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Assertions
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.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("030309 nutrition & dietetics")));
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}
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@Test
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void produceTest3Measures() throws Exception {
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final String doi = "unresolved::10.3390/s18072310::doi";
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JavaRDD<Result> tmp = getResultJavaRDD();
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Assertions
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.assertEquals(
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3, tmp
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.filter(row -> row.getId().equals(doi))
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.collect()
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.get(0)
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.getInstance()
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.get(0)
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.getMeasures()
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.size());
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List<Measure> measures = tmp
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.filter(row -> row.getId().equals(doi))
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.flatMap(row -> row.getInstance().iterator())
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.flatMap(inst -> inst.getMeasures().iterator())
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.collect();
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Assertions
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.assertEquals(
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"7.5597134689e-09", measures
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.stream()
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.filter(mes -> mes.getId().equals("influence"))
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.collect(Collectors.toList())
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.get(0)
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.getUnit()
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.get(0)
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.getValue());
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Assertions
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.assertEquals(
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"4.903880192", measures
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.stream()
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.filter(mes -> mes.getId().equals("popularity_alt"))
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.collect(Collectors.toList())
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.get(0)
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.getUnit()
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.get(0)
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.getValue());
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Assertions
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.assertEquals(
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"1.17977512835e-08", measures
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.stream()
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.filter(mes -> mes.getId().equals("popularity"))
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.collect(Collectors.toList())
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.get(0)
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.getUnit()
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.get(0)
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.getValue());
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Assertions
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.assertEquals(
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"10.3390/s18072310",
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tmp
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.filter(row -> row.getId().equals(doi))
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.collect()
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.get(0)
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.getInstance()
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.get(0)
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.getPid()
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.get(0)
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.getValue()
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.toLowerCase());
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Assertions
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.assertEquals(
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"doi",
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tmp
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.filter(row -> row.getId().equals(doi))
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.collect()
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.get(0)
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.getInstance()
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.get(0)
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.getPid()
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.get(0)
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.getQualifier()
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.getClassid());
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Assertions
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.assertEquals(
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"Digital Object Identifier",
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tmp
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.filter(row -> row.getId().equals(doi))
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.collect()
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.get(0)
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.getInstance()
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.get(0)
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.getPid()
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.get(0)
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.getQualifier()
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.getClassname());
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}
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@Test
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void produceTestMeasures() throws Exception {
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final String doi = "unresolved::10.3390/s18072310::doi";
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JavaRDD<Result> tmp = getResultJavaRDD();
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List<StructuredProperty> mes = tmp
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.filter(row -> row.getInstance() != null && row.getInstance().size() > 0)
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.flatMap(row -> row.getInstance().iterator())
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.flatMap(i -> i.getPid().iterator())
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.collect();
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Assertions.assertEquals(86, mes.size());
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tmp
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.filter(row -> row.getInstance() != null && row.getInstance().size() > 0)
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.foreach(
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e -> Assertions.assertEquals("sysimport:enrich", e.getDataInfo().getProvenanceaction().getClassid()));
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}
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@Test
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void produceTestSomeNumbers() throws Exception {
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final String doi = "unresolved::10.3390/s18072310::doi";
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JavaRDD<Result> tmp = getResultJavaRDD();
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Assertions.assertEquals(105, tmp.count());
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Assertions.assertEquals(1, tmp.filter(row -> row.getId().equals(doi)).count());
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Assertions
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.assertEquals(
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19, tmp
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.filter(row -> !row.getId().equals(doi))
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.filter(row -> row.getSubject() != null)
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.count());
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Assertions
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.assertEquals(
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85,
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tmp
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.filter(row -> !row.getId().equals(doi))
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.filter(r -> r.getInstance() != null && r.getInstance().size() > 0)
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.count());
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}
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private JavaRDD<Result> getResultJavaRDD() throws Exception {
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final String bipPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
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.getPath();
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PrepareBipFinder
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.main(
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new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--sourcePath", bipPath,
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"--outputPath", workingDir.toString() + "/work"
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});
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final String fosPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/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", fosPath,
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"-outputPath", workingDir.toString() + "/work"
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});
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SparkSaveUnresolved.main(new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--sourcePath", workingDir.toString() + "/work",
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"-outputPath", workingDir.toString() + "/unresolved"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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return sc
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.textFile(workingDir.toString() + "/unresolved")
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.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
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}
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@Test
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void prepareTest5Subjects() throws Exception {
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final String doi = "unresolved::10.1063/5.0032658::doi";
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JavaRDD<Result> tmp = getResultJavaRDD();
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Assertions.assertEquals(1, tmp.filter(row -> row.getId().equals(doi)).count());
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Assertions
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.assertEquals(
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5, tmp
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.filter(row -> row.getId().equals(doi))
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.collect()
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.get(0)
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.getSubject()
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.size());
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List<StructuredProperty> sbjs = tmp
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.filter(row -> row.getId().equals(doi))
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.flatMap(row -> row.getSubject().iterator())
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.collect();
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Assertions
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.assertEquals(
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true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("01 natural sciences")));
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Assertions.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0103 physical sciences")));
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Assertions
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.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("010304 chemical physics")));
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Assertions.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0104 chemical sciences")));
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Assertions
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.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("010402 general chemistry")));
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}
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private JavaRDD<Result> getResultJavaRDDPlusSDG() throws Exception {
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final String bipPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json")
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.getPath();
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PrepareBipFinder
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.main(
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new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--sourcePath", bipPath,
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"--outputPath", workingDir.toString() + "/work"
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});
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final String fosPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/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", fosPath,
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"-outputPath", workingDir.toString() + "/work"
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});
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final String sdgPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/sdg/sdg.json")
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.getPath();
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PrepareSDGSparkJob
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.main(
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new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--sourcePath", sdgPath,
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"-outputPath", workingDir.toString() + "/work"
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});
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SparkSaveUnresolved.main(new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--sourcePath", workingDir.toString() + "/work",
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"-outputPath", workingDir.toString() + "/unresolved"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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return sc
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.textFile(workingDir.toString() + "/unresolved")
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.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
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}
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@Test
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void produceTestSomeNumbersWithSDG() throws Exception {
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final String doi = "unresolved::10.3390/s18072310::doi";
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JavaRDD<Result> tmp = getResultJavaRDDPlusSDG();
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Assertions.assertEquals(136, tmp.count());
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Assertions.assertEquals(1, tmp.filter(row -> row.getId().equals(doi)).count());
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Assertions
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.assertEquals(
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50, tmp
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.filter(row -> !row.getId().equals(doi))
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.filter(row -> row.getSubject() != null)
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.count());
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Assertions
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.assertEquals(
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85,
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tmp
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.filter(row -> !row.getId().equals(doi))
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.filter(r -> r.getInstance() != null && r.getInstance().size() > 0)
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.count());
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}
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@Test
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void produceTest7Subjects() throws Exception {
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final String doi = "unresolved::10.3390/s18072310::doi";
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JavaRDD<Result> tmp = getResultJavaRDDPlusSDG();
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Assertions
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.assertEquals(
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7, tmp
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.filter(row -> row.getId().equals(doi))
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.collect()
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.get(0)
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.getSubject()
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.size());
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|
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List<StructuredProperty> sbjs = tmp
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.filter(row -> row.getId().equals(doi))
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.flatMap(row -> row.getSubject().iterator())
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.collect();
|
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|
|
Assertions
|
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.assertEquals(
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true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("04 agricultural and veterinary sciences")));
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|
|
Assertions
|
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.assertEquals(
|
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true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0404 agricultural biotechnology")));
|
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Assertions.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("040502 food science")));
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|
|
Assertions
|
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.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("03 medical and health sciences")));
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|
Assertions.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("0303 health sciences")));
|
|
Assertions
|
|
.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("030309 nutrition & dietetics")));
|
|
Assertions
|
|
.assertEquals(true, sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("1. No poverty")));
|
|
|
|
}
|
|
|
|
@Test
|
|
void produceTestSubjectsWithSDG() throws Exception {
|
|
|
|
JavaRDD<Result> tmp = getResultJavaRDDPlusSDG();
|
|
|
|
List<StructuredProperty> sbjs_sdg = tmp
|
|
.filter(row -> row.getSubject() != null && row.getSubject().size() > 0)
|
|
.flatMap(row -> row.getSubject().iterator())
|
|
.filter(sbj -> sbj.getQualifier().getClassid().equals(Constants.SDG_CLASS_ID))
|
|
.collect();
|
|
|
|
sbjs_sdg.forEach(sbj -> Assertions.assertEquals("SDG", sbj.getQualifier().getClassid()));
|
|
sbjs_sdg
|
|
.forEach(
|
|
sbj -> Assertions
|
|
.assertEquals(
|
|
"Sustainable Development Goals", sbj.getQualifier().getClassname()));
|
|
sbjs_sdg
|
|
.forEach(
|
|
sbj -> Assertions
|
|
.assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemeid()));
|
|
sbjs_sdg
|
|
.forEach(
|
|
sbj -> Assertions
|
|
.assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemename()));
|
|
|
|
sbjs_sdg.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getDeletedbyinference()));
|
|
sbjs_sdg.forEach(sbj -> Assertions.assertEquals(true, sbj.getDataInfo().getInferred()));
|
|
sbjs_sdg.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getInvisible()));
|
|
sbjs_sdg.forEach(sbj -> Assertions.assertEquals("", sbj.getDataInfo().getTrust()));
|
|
sbjs_sdg.forEach(sbj -> Assertions.assertEquals("update", sbj.getDataInfo().getInferenceprovenance()));
|
|
sbjs_sdg
|
|
.forEach(
|
|
sbj -> Assertions.assertEquals("subject:sdg", sbj.getDataInfo().getProvenanceaction().getClassid()));
|
|
sbjs_sdg
|
|
.forEach(
|
|
sbj -> Assertions
|
|
.assertEquals("Inferred by OpenAIRE", sbj.getDataInfo().getProvenanceaction().getClassname()));
|
|
sbjs_sdg
|
|
.forEach(
|
|
sbj -> Assertions
|
|
.assertEquals(
|
|
ModelConstants.DNET_PROVENANCE_ACTIONS, sbj.getDataInfo().getProvenanceaction().getSchemeid()));
|
|
sbjs_sdg
|
|
.forEach(
|
|
sbj -> Assertions
|
|
.assertEquals(
|
|
ModelConstants.DNET_PROVENANCE_ACTIONS,
|
|
sbj.getDataInfo().getProvenanceaction().getSchemename()));
|
|
}
|
|
|
|
}
|