forked from D-Net/dnet-hadoop
488 lines
16 KiB
Java
488 lines
16 KiB
Java
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package eu.dnetlib.dhp.patchrefereed;
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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.Arrays;
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import java.util.List;
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import org.apache.commons.io.FileUtils;
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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.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.Row;
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import org.apache.spark.sql.SparkSession;
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import org.junit.jupiter.api.AfterAll;
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import org.junit.jupiter.api.Assertions;
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import org.junit.jupiter.api.BeforeAll;
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import org.junit.jupiter.api.Test;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import jdk.nashorn.internal.ir.annotations.Ignore;
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public class PatchRefereedTest {
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private static final Logger log = LoggerFactory.getLogger(PatchRefereedTest.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static SparkSession spark;
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private static Path workingDir;
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(PatchRefereedTest.class.getSimpleName());
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log.info("using work dir {}", workingDir);
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SparkConf conf = new SparkConf();
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conf.setAppName(PatchRefereedTest.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(PatchRefereedTest.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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public void test2() throws Exception {
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SparkPatchRefereed
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-inputPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/simpleTest/prod_publication.json").getPath(),
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-outputPath", workingDir.toString() + "/publication",
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"-preparedInfoPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/simpleTest/preparedInfo3.json").getPath()
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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(1, tmp.count());
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org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
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verificationDataset.createOrReplaceTempView("dataset");
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Dataset<Row> tmp1 = spark.sql("select inst.refereed from dataset lateral view explode(instance) i as inst");
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Assertions.assertEquals(1, tmp1.count());
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Assertions.assertEquals(1, tmp1.filter("refereed.classname = 'Unknown'").count());
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Assertions.assertEquals(1, tmp1.filter("refereed.classid = '0000'").count());
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}
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@Test
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public void test3() throws Exception {
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SparkPatchRefereed
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-inputPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/simpleTest/prod_publication.json").getPath(),
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-outputPath", workingDir.toString() + "/publication",
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"-preparedInfoPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/simpleTest/preparedInfo2.json").getPath()
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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(1, tmp.count());
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org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
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verificationDataset.createOrReplaceTempView("dataset");
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Dataset<Row> tmp1 = spark.sql("select inst.refereed from dataset lateral view explode(instance) i as inst");
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Assertions.assertEquals(1, tmp1.count());
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Assertions.assertEquals(1, tmp1.filter("refereed.classname = 'Unknown'").count());
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Assertions.assertEquals(1, tmp1.filter("refereed.classid = '0000'").count());
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}
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@Test
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public void test4() throws Exception {
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SparkPatchRefereed
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-inputPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/simpleTest/prod_publication.json").getPath(),
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-outputPath", workingDir.toString() + "/publication",
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"-preparedInfoPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/simpleTest/preparedInfo3.json").getPath()
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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(1, tmp.count());
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org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
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verificationDataset.createOrReplaceTempView("dataset");
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Dataset<Row> tmp1 = spark.sql("select inst.refereed from dataset lateral view explode(instance) i as inst");
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Assertions.assertEquals(1, tmp1.count());
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Assertions.assertEquals(1, tmp1.filter("refereed.classname = 'Unknown'").count());
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Assertions.assertEquals(1, tmp1.filter("refereed.classid = '0000'").count());
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}
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@Test
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public void test5() throws Exception {
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SparkPatchRefereed
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-inputPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/simpleTest/prod_publication2.json").getPath(),
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-outputPath", workingDir.toString() + "/publication",
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"-preparedInfoPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/simpleTest/preparedInfo4.json").getPath()
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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(1, tmp.count());
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org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
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verificationDataset.createOrReplaceTempView("dataset");
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Dataset<Row> tmp1 = spark.sql("select inst.refereed from dataset lateral view explode(instance) i as inst");
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Assertions.assertEquals(1, tmp1.count());
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Assertions.assertEquals(1, tmp1.filter("refereed.classname = 'PeerReviewd'").count());
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Assertions.assertEquals(1, tmp1.filter("refereed.classid = '0001'").count());
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}
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@Test
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public void test6() throws Exception {
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SparkPatchRefereed
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-inputPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/simpleTest/prod_publication1.json").getPath(),
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-outputPath", workingDir.toString() + "/publication",
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"-preparedInfoPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/simpleTest/preparedInfo4.json").getPath()
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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(1, tmp.count());
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org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
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verificationDataset.createOrReplaceTempView("dataset");
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Dataset<Row> tmp1 = spark.sql("select inst.refereed from dataset lateral view explode(instance) i as inst");
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Assertions.assertEquals(1, tmp1.count());
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Assertions.assertEquals(1, tmp1.filter("refereed.classname = 'Unknown'").count());
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Assertions.assertEquals(1, tmp1.filter("refereed.classid = '0000'").count());
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}
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@Test
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public void test8() throws Exception {
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SparkPatchRefereed
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-inputPath",
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getClass()
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.getResource("/eu/dnetlib/dhp/patchrefereed/test/noMatchUrlLen/prod_publication.json")
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.getPath(),
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-outputPath", workingDir.toString() + "/publication",
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"-preparedInfoPath",
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getClass()
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.getResource("/eu/dnetlib/dhp/patchrefereed/test/noMatchUrlLen/preparedInfo.json")
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.getPath()
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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(3, tmp.count());
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org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
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verificationDataset.createOrReplaceTempView("dataset");
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Dataset<Row> tmp1 = spark.sql("select inst.refereed from dataset lateral view explode(instance) i as inst");
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Assertions.assertEquals(3, tmp1.count());
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Assertions.assertEquals(3, tmp1.filter("refereed.classname = 'Unknown' and refereed.classid ='0000'").count());
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}
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@Test
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public void test7() throws Exception {
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SparkPatchRefereed
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-inputPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/test/match1/prod_publication.json").getPath(),
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-outputPath", workingDir.toString() + "/publication",
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"-preparedInfoPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/test/match1/preparedInfo.json").getPath()
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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(3, tmp.count());
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org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
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verificationDataset.createOrReplaceTempView("dataset");
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Dataset<Row> tmp1 = spark.sql("select inst.refereed from dataset lateral view explode(instance) i as inst");
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Assertions.assertEquals(3, tmp1.count());
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Assertions.assertEquals(1, tmp1.filter("refereed.classname = 'Unknown' and refereed.classid ='0000'").count());
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Assertions
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.assertEquals(1, tmp1.filter("refereed.classname = 'PeerReviewd' and refereed.classid ='0001'").count());
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Assertions
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.assertEquals(1, tmp1.filter("refereed.classname = 'NonPeerReviewd' and refereed.classid ='0002'").count());
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}
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@Test
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public void test9() throws Exception {
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SparkPatchRefereed
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-inputPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/test/match2/prod_publication.json").getPath(),
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-outputPath", workingDir.toString() + "/publication",
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"-preparedInfoPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/test/match2/preparedInfo.json").getPath()
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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(3, tmp.count());
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org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
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verificationDataset.createOrReplaceTempView("dataset");
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Dataset<Row> tmp1 = spark.sql("select id, inst.refereed from dataset lateral view explode(instance) i as inst");
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Assertions.assertEquals(4, tmp1.count());
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Assertions.assertEquals(3, tmp1.filter("refereed.classname = 'Unknown' and refereed.classid ='0000'").count());
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Assertions
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.assertEquals(1, tmp1.filter("refereed.classname = 'PeerReviewd' and refereed.classid ='0001'").count());
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Assertions
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.assertEquals(
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1, tmp1
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.filter(
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"id = '50|orcid_______::6c6960227e2775a019090d8f33e0e6e5' and " +
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"refereed.classname = 'PeerReviewd' and refereed.classid ='0001'")
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.count());
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Assertions
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.assertEquals(
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1, tmp1
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.filter(
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"id = '50|orcid_______::6c6960227e2775a019090d8f33e0e6e5' and " +
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"refereed.classname = 'Unknown' and refereed.classid ='0000'")
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.count());
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}
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@Test
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public void test10() throws Exception {
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SparkPatchRefereed
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-inputPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/test/match3/prod_publication.json").getPath(),
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-outputPath", workingDir.toString() + "/publication",
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"-preparedInfoPath",
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getClass().getResource("/eu/dnetlib/dhp/patchrefereed/test/match3/preparedInfo.json").getPath()
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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(4, tmp.count());
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org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
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verificationDataset.createOrReplaceTempView("dataset");
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Dataset<Row> tmp1 = spark.sql("select id, inst.refereed from dataset lateral view explode(instance) i as inst");
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Assertions.assertEquals(4, tmp1.count());
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tmp1.show(false);
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Assertions.assertEquals(2, tmp1.filter("refereed.classname = 'Unknown' and refereed.classid ='0000'").count());
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Assertions
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.assertEquals(
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2, tmp1.filter("refereed.classname = 'nonPeerReviewed' and refereed.classid ='0002'").count());
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Assertions
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.assertEquals(
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1, tmp1
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.filter(
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"id = '50|core_ac_uk__::05d41a3ffee162ae2561befeb718ccf7' and " +
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"refereed.classname = 'Unknown' and refereed.classid ='0000' ")
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.count());
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Assertions
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.assertEquals(
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1, tmp1
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.filter(
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"id = '50|core_ac_uk__::b32ca62afc4299e1f43515bc3c33b58f' and " +
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"refereed.classname = 'Unknown' and refereed.classid ='0000'")
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.count());
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Assertions
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.assertEquals(
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1, tmp1
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.filter(
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"id = '50|core_ac_uk__::127d5c16ad41fe6cf2d196abbae5596e' and " +
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"refereed.classname = 'nonPeerReviewed' and refereed.classid ='0002' ")
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.count());
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Assertions
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.assertEquals(
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1, tmp1
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.filter(
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"id = '50|core_ac_uk__::4810ff7dc1a3db8c2568d5fe7245e067' and " +
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"refereed.classname = 'nonPeerReviewed' and refereed.classid ='0002'")
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.count());
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}
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@Test
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public void remove() {
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KeyValue cf1 = new KeyValue();
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KeyValue cf2 = new KeyValue();
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cf1.setKey("10|openaire____::0a836ef43dcb67bb7cbd4dd509b11b73");
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cf1.setValue("CORE (RIOXX-UK Aggregator)");
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cf2.setKey("10|openaire____::0a836ef43dcb67bb7cbd4dd509b11b73");
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cf2.setValue("CORE (RIOXX-UK Aggregator)");
|
|
|
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System.out.println(cf1.equals(cf2));
|
|
|
|
List<String> url1 = Arrays.asList("http://wrap.warwick.ac.uk/66746/1/WRAP_THESIS_Ritchie_2014.pdf");
|
|
|
|
List<String> url2 = Arrays.asList("http://wrap.warwick.ac.uk/66746/1/WRAP_THESIS_Ritchie_2014.pdf");
|
|
|
|
System.out.println(SparkPatchRefereed.equals(url1, url2));
|
|
}
|
|
}
|