2021-09-27 16:02:06 +02:00
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package eu.dnetlib.dhp.actionmanager.opencitations;
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import static org.junit.jupiter.api.Assertions.assertEquals;
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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 org.apache.commons.io.FileUtils;
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import org.apache.hadoop.io.Text;
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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.action.AtomicAction;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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public class CreateOpenCitationsASTest {
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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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private static final Logger log = LoggerFactory
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.getLogger(CreateOpenCitationsASTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files
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.createTempDirectory(CreateOpenCitationsASTest.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(CreateOpenCitationsASTest.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(CreateOpenCitationsASTest.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 testNumberofRelations() throws Exception {
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String inputPath = getClass()
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.getResource(
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2022-02-07 18:32:08 +01:00
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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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2021-09-27 16:02:06 +02:00
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.getPath();
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CreateActionSetSparkJob
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.main(
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new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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2021-11-15 17:07:16 +01:00
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"-shouldDuplicateRels",
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Boolean.TRUE.toString(),
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2021-09-27 16:02:06 +02:00
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"-inputPath",
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inputPath,
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"-outputPath",
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2021-12-06 15:27:09 +01:00
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workingDir.toString() + "/actionSet1"
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2021-09-27 16:02:06 +02:00
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Relation> tmp = sc
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2021-12-06 15:27:09 +01:00
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.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
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2021-09-27 16:02:06 +02:00
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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.map(aa -> ((Relation) aa.getPayload()));
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2022-02-07 18:32:08 +01:00
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assertEquals(62, tmp.count());
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2021-09-27 16:02:06 +02:00
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2021-11-15 17:07:16 +01:00
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// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
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2021-10-18 14:11:27 +02:00
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}
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@Test
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void testNumberofRelations2() throws Exception {
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String inputPath = getClass()
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2021-11-15 17:07:16 +01:00
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.getResource(
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2022-02-07 18:32:08 +01:00
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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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2021-11-15 17:07:16 +01:00
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.getPath();
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2021-10-18 14:11:27 +02:00
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CreateActionSetSparkJob
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2021-11-15 17:07:16 +01:00
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.main(
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new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-inputPath",
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inputPath,
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"-outputPath",
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2021-12-06 15:27:09 +01:00
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workingDir.toString() + "/actionSet2"
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2021-11-15 17:07:16 +01:00
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});
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2021-10-18 14:11:27 +02:00
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Relation> tmp = sc
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2021-12-06 15:27:09 +01:00
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.sequenceFile(workingDir.toString() + "/actionSet2", Text.class, Text.class)
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2021-11-15 17:07:16 +01:00
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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.map(aa -> ((Relation) aa.getPayload()));
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2021-10-18 14:11:27 +02:00
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2022-02-07 18:32:08 +01:00
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assertEquals(46, tmp.count());
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2021-10-18 14:11:27 +02:00
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2021-11-15 17:07:16 +01:00
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// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
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2021-09-27 16:02:06 +02:00
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}
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@Test
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void testRelationsCollectedFrom() throws Exception {
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String inputPath = getClass()
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.getResource(
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2022-02-07 18:32:08 +01:00
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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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2021-09-27 16:02:06 +02:00
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.getPath();
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CreateActionSetSparkJob
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.main(
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new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-inputPath",
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inputPath,
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"-outputPath",
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2021-12-06 15:27:09 +01:00
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workingDir.toString() + "/actionSet3"
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2021-09-27 16:02:06 +02:00
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Relation> tmp = sc
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2021-12-06 15:27:09 +01:00
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.sequenceFile(workingDir.toString() + "/actionSet3", Text.class, Text.class)
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2021-09-27 16:02:06 +02:00
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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.map(aa -> ((Relation) aa.getPayload()));
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tmp.foreach(r -> {
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assertEquals(ModelConstants.OPENOCITATIONS_NAME, r.getCollectedfrom().get(0).getValue());
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assertEquals(ModelConstants.OPENOCITATIONS_ID, r.getCollectedfrom().get(0).getKey());
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});
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}
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@Test
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void testRelationsDataInfo() throws Exception {
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String inputPath = getClass()
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.getResource(
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2022-02-07 18:32:08 +01:00
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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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2021-09-27 16:02:06 +02:00
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.getPath();
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CreateActionSetSparkJob
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.main(
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new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-inputPath",
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inputPath,
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"-outputPath",
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2021-12-06 15:27:09 +01:00
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workingDir.toString() + "/actionSet4"
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2021-09-27 16:02:06 +02:00
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Relation> tmp = sc
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2021-12-06 15:27:09 +01:00
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.sequenceFile(workingDir.toString() + "/actionSet4", Text.class, Text.class)
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2021-09-27 16:02:06 +02:00
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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.map(aa -> ((Relation) aa.getPayload()));
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tmp.foreach(r -> {
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assertEquals(false, r.getDataInfo().getInferred());
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assertEquals(false, r.getDataInfo().getDeletedbyinference());
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assertEquals("0.91", r.getDataInfo().getTrust());
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assertEquals(
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CreateActionSetSparkJob.OPENCITATIONS_CLASSID, r.getDataInfo().getProvenanceaction().getClassid());
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assertEquals(
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CreateActionSetSparkJob.OPENCITATIONS_CLASSNAME, r.getDataInfo().getProvenanceaction().getClassname());
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assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemeid());
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assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemename());
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});
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}
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@Test
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void testRelationsSemantics() throws Exception {
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String inputPath = getClass()
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.getResource(
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2022-02-07 18:32:08 +01:00
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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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2021-09-27 16:02:06 +02:00
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.getPath();
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CreateActionSetSparkJob
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.main(
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new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-inputPath",
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inputPath,
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"-outputPath",
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2021-12-06 15:27:09 +01:00
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workingDir.toString() + "/actionSet5"
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2021-09-27 16:02:06 +02:00
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Relation> tmp = sc
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2021-12-06 15:27:09 +01:00
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.sequenceFile(workingDir.toString() + "/actionSet5", Text.class, Text.class)
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2021-09-27 16:02:06 +02:00
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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.map(aa -> ((Relation) aa.getPayload()));
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tmp.foreach(r -> {
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assertEquals("citation", r.getSubRelType());
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assertEquals("resultResult", r.getRelType());
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});
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assertEquals(23, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
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assertEquals(23, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
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2021-09-27 16:02:06 +02:00
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}
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@Test
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void testRelationsSourceTargetPrefix() throws Exception {
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String inputPath = getClass()
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.getResource(
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2022-02-07 18:32:08 +01:00
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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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2021-09-27 16:02:06 +02:00
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.getPath();
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CreateActionSetSparkJob
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.main(
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new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-inputPath",
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inputPath,
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"-outputPath",
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2021-12-06 15:27:09 +01:00
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workingDir.toString() + "/actionSet6"
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Relation> tmp = sc
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2021-12-06 15:27:09 +01:00
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.sequenceFile(workingDir.toString() + "/actionSet6", Text.class, Text.class)
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2021-09-27 16:02:06 +02:00
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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.map(aa -> ((Relation) aa.getPayload()));
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tmp.foreach(r -> {
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assertEquals("50|doi_________::", r.getSource().substring(0, 17));
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assertEquals("50|doi_________::", r.getTarget().substring(0, 17));
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});
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}
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@Test
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void testRelationsSourceTargetCouple() throws Exception {
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final String doi1 = "50|doi_________::"
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-015-3684-x"));
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final String doi2 = "50|doi_________::"
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x"));
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final String doi3 = "50|doi_________::"
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-014-2114-9"));
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final String doi4 = "50|doi_________::"
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069"));
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final String doi5 = "50|doi_________::"
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-009-9913-4"));
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final String doi6 = "50|doi_________::"
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5"));
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String inputPath = getClass()
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.getResource(
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2022-02-07 18:32:08 +01:00
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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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2021-09-27 16:02:06 +02:00
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.getPath();
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CreateActionSetSparkJob
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.main(
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new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-inputPath",
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inputPath,
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"-outputPath",
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workingDir.toString() + "/actionSet7"
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Relation> tmp = sc
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2021-12-06 15:27:09 +01:00
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.sequenceFile(workingDir.toString() + "/actionSet7", Text.class, Text.class)
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2021-09-27 16:02:06 +02:00
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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.map(aa -> ((Relation) aa.getPayload()));
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JavaRDD<Relation> check = tmp.filter(r -> r.getSource().equals(doi1) || r.getTarget().equals(doi1));
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assertEquals(10, check.count());
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check.foreach(r -> {
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if (r.getSource().equals(doi2) || r.getSource().equals(doi3) || r.getSource().equals(doi4) ||
|
|
|
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r.getSource().equals(doi5) || r.getSource().equals(doi6)) {
|
|
|
|
assertEquals(ModelConstants.IS_CITED_BY, r.getRelClass());
|
|
|
|
assertEquals(doi1, r.getTarget());
|
|
|
|
}
|
|
|
|
});
|
|
|
|
|
|
|
|
assertEquals(5, check.filter(r -> r.getSource().equals(doi1)).count());
|
|
|
|
check.filter(r -> r.getSource().equals(doi1)).foreach(r -> assertEquals(ModelConstants.CITES, r.getRelClass()));
|
|
|
|
|
|
|
|
}
|
|
|
|
}
|