286 lines
12 KiB
Java
286 lines
12 KiB
Java
package eu.dnetlib.dhp.actionmanager.webcrawl;
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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 eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
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import eu.dnetlib.dhp.schema.oaf.utils.PidType;
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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.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.oaf.Relation;
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/**
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* @author miriam.baglioni
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* @Date 22/04/24
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*/
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public class CreateASTest {
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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(CreateASTest.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(CreateASTest.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(CreateASTest.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(CreateASTest.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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"/eu/dnetlib/dhp/actionmanager/webcrawl/")
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.getPath();
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CreateActionSetFromWebEntries
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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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"-sourcePath",
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inputPath,
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"-outputPath",
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workingDir.toString() + "/actionSet1"
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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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.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
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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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Assertions.assertEquals(64, tmp.count());
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}
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@Test
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void testRelations() throws Exception {
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// , "doi":"https://doi.org/10.1126/science.1188021", "pmid":"https://pubmed.ncbi.nlm.nih.gov/20448178", https://www.ncbi.nlm.nih.gov/pmc/articles/5100745
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String inputPath = getClass()
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.getResource(
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"/eu/dnetlib/dhp/actionmanager/webcrawl/")
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.getPath();
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CreateActionSetFromWebEntries
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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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"-sourcePath",
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inputPath,
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"-outputPath",
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workingDir.toString() + "/actionSet1"
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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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.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
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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 -> System.out.println(new ObjectMapper().writeValueAsString(r)));
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Assertions
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.assertEquals(
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1, tmp
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.filter(
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r -> r
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.getSource()
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.equals(
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"50|doi_________::" + IdentifierFactory
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.md5(
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PidCleaner
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.normalizePidValue(PidType.doi.toString(), "10.1098/rstl.1684.0023"))))
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.count());
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Assertions
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.assertEquals(
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1, tmp
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.filter(
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r -> r
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.getTarget()
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.equals(
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"50|doi_________::" + IdentifierFactory
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.md5(
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PidCleaner
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.normalizePidValue(PidType.doi.toString(), "10.1098/rstl.1684.0023"))))
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.count());
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Assertions
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.assertEquals(
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1, tmp
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.filter(
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r -> r
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.getSource()
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.equals(
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"20|ror_________::" + IdentifierFactory
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.md5(
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PidCleaner
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.normalizePidValue("ROR", "https://ror.org/03argrj65"))))
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.count());
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Assertions
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.assertEquals(
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1, tmp
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.filter(
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r -> r
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.getTarget()
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.equals(
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"20|ror_________::" + IdentifierFactory
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.md5(
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PidCleaner
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.normalizePidValue("ROR", "https://ror.org/03argrj65"))))
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.count());
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Assertions
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.assertEquals(
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5, tmp
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.filter(
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r -> r
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.getSource()
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.equals(
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"20|ror_________::" + IdentifierFactory
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.md5(
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PidCleaner
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.normalizePidValue("ROR", "https://ror.org/03265fv13"))))
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.count());
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Assertions
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.assertEquals(
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5, tmp
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.filter(
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r -> r
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.getTarget()
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.equals(
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"20|ror_________::" + IdentifierFactory
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.md5(
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PidCleaner
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.normalizePidValue("ROR", "https://ror.org/03265fv13"))))
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.count());
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Assertions
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.assertEquals(
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2, tmp
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.filter(
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r -> r
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.getTarget()
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.equals(
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"20|ror_________::" + IdentifierFactory
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.md5(
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PidCleaner
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.normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13")))
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&& r.getSource().startsWith("50|doi"))
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.count());
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Assertions
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.assertEquals(
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2, tmp
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.filter(
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r -> r
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.getTarget()
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.equals(
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"20|ror_________::" + IdentifierFactory
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.md5(
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PidCleaner
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.normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13")))
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&& r.getSource().startsWith("50|pmid"))
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.count());
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Assertions
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.assertEquals(
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1, tmp
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.filter(
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r -> r
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.getTarget()
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.equals(
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"20|ror_________::" + IdentifierFactory
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.md5(
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PidCleaner
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.normalizePidValue(PidType.doi.toString(), "https://ror.org/03265fv13")))
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&& r.getSource().startsWith("50|pmc"))
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.count());
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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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"/eu/dnetlib/dhp/actionmanager/webcrawl")
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.getPath();
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CreateActionSetFromWebEntries
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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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"-sourcePath",
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inputPath,
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"-outputPath",
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workingDir.toString() + "/actionSet1"
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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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.sequenceFile(workingDir.toString() + "/actionSet1", Text.class, Text.class)
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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("Web Crawl", r.getCollectedfrom().get(0).getValue());
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assertEquals("10|openaire____::fb98a192f6a055ba495ef414c330834b", r.getCollectedfrom().get(0).getKey());
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});
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}
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}
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