328 lines
9.4 KiB
Java
328 lines
9.4 KiB
Java
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package eu.dnetlib.dhp.actionmanager.createunresolvedentities;
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import static org.junit.jupiter.api.Assertions.*;
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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.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.*;
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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.createunresolvedentities.model.FOSDataModel;
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import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.SDGDataModel;
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import eu.dnetlib.dhp.schema.oaf.Result;
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public class PrepareTest {
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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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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(PrepareTest.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(PrepareTest.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 bipPrepareTest() throws Exception {
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final String sourcePath = 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", sourcePath,
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"--outputPath", workingDir.toString() + "/work"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Result> tmp = sc
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.textFile(workingDir.toString() + "/work/bip")
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.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
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Assertions.assertEquals(87, tmp.count());
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String doi1 = "unresolved::10.0000/096020199389707::doi";
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Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).count());
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Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getInstance().size());
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Assertions
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.assertEquals(
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3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getInstance().get(0).getMeasures().size());
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Assertions
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.assertEquals(
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"6.34596412687e-09", tmp
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.filter(r -> r.getId().equals(doi1))
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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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.stream()
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.filter(sl -> sl.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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"0.641151896994", tmp
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.filter(r -> r.getId().equals(doi1))
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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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.stream()
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.filter(sl -> sl.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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"2.33375102921e-09", tmp
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.filter(r -> r.getId().equals(doi1))
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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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.stream()
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.filter(sl -> sl.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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final String doi2 = "unresolved::10.3390/s18072310::doi";
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Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).count());
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Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi2)).collect().get(0).getInstance().size());
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tmp.filter(r -> r.getId().startsWith("unresolved::10.2111/1551-5028(2004)057"))
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.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
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}
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@Test
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void fosPrepareTest() throws Exception {
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final String sourcePath = 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", sourcePath,
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"-outputPath", workingDir.toString() + "/work"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Result> tmp = sc
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.textFile(workingDir.toString() + "/work/fos")
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.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
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String doi1 = "unresolved::10.3390/s18072310::doi";
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assertEquals(20, tmp.count());
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assertEquals(1, tmp.filter(row -> row.getId().equals(doi1)).count());
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assertTrue(
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tmp
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.filter(r -> r.getId().equals(doi1))
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.flatMap(r -> r.getSubject().iterator())
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.map(sbj -> sbj.getValue())
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.collect()
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.contains("04 agricultural and veterinary sciences"));
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assertTrue(
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tmp
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.filter(r -> r.getId().equals(doi1))
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.flatMap(r -> r.getSubject().iterator())
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.map(sbj -> sbj.getValue())
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.collect()
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.contains("0404 agricultural biotechnology"));
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String doi = "unresolved::10.1007/s11164-020-04383-6::doi";
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assertEquals(1, tmp.filter(row -> row.getId().equals(doi)).count());
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assertTrue(
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tmp
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.filter(r -> r.getId().equals(doi))
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.flatMap(r -> r.getSubject().iterator())
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.map(sbj -> sbj.getValue())
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.collect()
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.contains("01 natural sciences"));
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assertTrue(
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tmp
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.filter(r -> r.getId().equals(doi))
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.flatMap(r -> r.getSubject().iterator())
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.map(sbj -> sbj.getValue())
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.collect()
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.contains("0104 chemical sciences"));
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assertTrue(
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tmp
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.filter(r -> r.getId().equals(doi))
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.flatMap(r -> r.getSubject().iterator())
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.map(sbj -> sbj.getValue())
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.collect()
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.contains("010402 general chemistry"));
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}
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@Test
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void sdgPrepareTest() throws Exception {
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final String sourcePath = 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", sourcePath,
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"-outputPath", workingDir.toString() + "/work"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Result> tmp = sc
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.textFile(workingDir.toString() + "/work/sdg")
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.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
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String doi1 = "unresolved::10.1001/amaguidesnewsletters.2019.sepoct02::doi";
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assertEquals(32, tmp.count());
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assertEquals(1, tmp.filter(row -> row.getId().equals(doi1)).count());
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assertTrue(
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tmp
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.filter(r -> r.getId().equals(doi1))
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.flatMap(r -> r.getSubject().iterator())
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.map(sbj -> sbj.getValue())
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.collect()
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.contains("3. Good health"));
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assertTrue(
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tmp
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.filter(r -> r.getId().equals(doi1))
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.flatMap(r -> r.getSubject().iterator())
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.map(sbj -> sbj.getValue())
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.collect()
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.contains("8. Economic growth"));
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Assertions.assertEquals(32, tmp.filter(row -> row.getDataInfo() != null).count());
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}
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// @Test
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// void test3() throws Exception {
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// final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_fos_results_20_12_2021.csv.gz";
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//
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// final String outputPath = workingDir.toString() + "/fos.json";
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// GetFOSSparkJob
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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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//
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// "-outputPath", outputPath
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//
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// });
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//
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// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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//
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// JavaRDD<FOSDataModel> tmp = sc
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// .textFile(outputPath)
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// .map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
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//
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// tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
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// tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null));
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// tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null));
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// tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null));
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//
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// }
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//
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// @Test
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// void test4() throws Exception {
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// final String sourcePath = "/Users/miriam.baglioni/Downloads/doi_sdg_results_20_12_21.csv.gz";
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//
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// final String outputPath = workingDir.toString() + "/sdg.json";
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// GetSDGSparkJob
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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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//
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// "-outputPath", outputPath
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//
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// });
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//
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// final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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//
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// JavaRDD<SDGDataModel> tmp = sc
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// .textFile(outputPath)
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// .map(item -> OBJECT_MAPPER.readValue(item, SDGDataModel.class));
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//
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// tmp.foreach(t -> Assertions.assertTrue(t.getDoi() != null));
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// tmp.foreach(t -> Assertions.assertTrue(t.getSbj() != null));
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//
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// }
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}
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