forked from D-Net/dnet-hadoop
256 lines
7.1 KiB
Java
256 lines
7.1 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 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 fosPrepareTest2() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos_sbs_2.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::10.1016/j.revmed.2006.07.012::doi";
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assertEquals(13, tmp.count());
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assertEquals(1, tmp.filter(row -> row.getId().equals(doi1)).count());
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Result result = tmp
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.filter(r -> r.getId().equals(doi1))
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.first();
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result.getSubject().forEach(s -> System.out.println(s.getValue() + " trust = " + s.getDataInfo().getTrust()));
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Assertions.assertEquals(6, result.getSubject().size());
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assertTrue(
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result
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.getSubject()
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.stream()
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.anyMatch(
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s -> s.getValue().contains("03 medical and health sciences")
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&& s.getDataInfo().getTrust().equals("")));
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assertTrue(
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result
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.getSubject()
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.stream()
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.anyMatch(
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s -> s.getValue().contains("0302 clinical medicine") && s.getDataInfo().getTrust().equals("")));
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assertTrue(
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result
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.getSubject()
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.stream()
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.anyMatch(
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s -> s
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.getValue()
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.contains("030204 cardiovascular system & hematology")
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&& s.getDataInfo().getTrust().equals("0.5101401805877686")));
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assertTrue(
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result
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.getSubject()
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.stream()
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.anyMatch(
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s -> s
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.getValue()
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.contains("03020409 Hematology/Coagulopathies")
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&& s.getDataInfo().getTrust().equals("0.0546871414174914")));
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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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}
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