148 lines
4.6 KiB
Java
148 lines
4.6 KiB
Java
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package eu.dnetlib.dhp.actionmanager.bipaffiliations;
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import static org.junit.jupiter.api.Assertions.*;
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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.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 PrepareAffiliationRelationsTest {
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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 String ID_PREFIX = "50|doi_________::";
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private static final Logger log = LoggerFactory
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.getLogger(PrepareAffiliationRelationsTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(PrepareAffiliationRelationsTest.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(PrepareAffiliationRelationsTest.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(PrepareAffiliationRelationsTest.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 testMatch() throws Exception {
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String crossrefAffiliationRelationPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipaffiliations/doi_to_ror.json")
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.getPath();
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String outputPath = workingDir.toString() + "/actionSet";
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PrepareAffiliationRelations
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-crossrefInputPath", crossrefAffiliationRelationPath,
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"-pubmedInputPath", crossrefAffiliationRelationPath,
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"-openapcInputPath", crossrefAffiliationRelationPath,
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"-outputPath", outputPath
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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(outputPath, 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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// for (Relation r : tmp.collect()) {
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// System.out.println(
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// r.getSource() + "\t" + r.getTarget() + "\t" + r.getRelType() + "\t" + r.getRelClass() + "\t" + r.getSubRelType() + "\t" + r.getValidationDate() + "\t" + r.getDataInfo().getTrust() + "\t" + r.getDataInfo().getInferred()
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// );
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// }
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// count the number of relations
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assertEquals(60, tmp.count());
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Dataset<Relation> dataset = spark.createDataset(tmp.rdd(), Encoders.bean(Relation.class));
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dataset.createOrReplaceTempView("result");
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Dataset<Row> execVerification = spark
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.sql("select r.relType, r.relClass, r.source, r.target, r.dataInfo.trust from result r");
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// verify that we have equal number of bi-directional relations
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Assertions
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.assertEquals(
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30, execVerification
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.filter(
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"relClass='" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
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.collectAsList()
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.size());
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Assertions
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.assertEquals(
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30, execVerification
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.filter(
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"relClass='" + ModelConstants.IS_AUTHOR_INSTITUTION_OF + "'")
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.collectAsList()
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.size());
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// check confidence value of a specific relation
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String sourceDOI = "10.1061/(asce)0733-9399(2002)128:7(759)";
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final String sourceOpenaireId = ID_PREFIX
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", sourceDOI));
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Assertions
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.assertEquals(
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"0.7071067812", execVerification
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.filter(
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"source='" + sourceOpenaireId + "'")
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.collectAsList()
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.get(0)
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.getString(4));
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}
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}
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