208 lines
5.7 KiB
Java
208 lines
5.7 KiB
Java
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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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.neethi.Assertion;
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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.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 com.google.gson.Gson;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.Dataset;
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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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public class PrepareStep1Test {
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private static final Logger log = LoggerFactory.getLogger(PrepareStep1Test.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(PrepareStep1Test.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(PrepareStep1Test.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("spark.ui.enabled", "false");
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conf.set("spark.sql.warehouse.dir", workingDir.toString());
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spark = SparkSession
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.builder()
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.appName(PrepareStep1Test.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 noMatchTest() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparestep1")
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.getPath();
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PrepareResultOrcidAssociationStep1
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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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"-resultTableName", Dataset.class.getCanonicalName(),
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"-outputPath", workingDir.toString() + "/preparedInfo",
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"-allowedsemrels", "IsSupplementedBy;IsSupplementTo",
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"-allowedpids", "orcid;orcid_pending"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<ResultOrcidList> tmp = sc
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.textFile(workingDir.toString() + "/preparedInfo/dataset")
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.map(item -> OBJECT_MAPPER.readValue(item, ResultOrcidList.class));
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Assertions.assertEquals(0, tmp.count());
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Assertions
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.assertEquals(
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7, sc
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.textFile(workingDir.toString() + "/preparedInfo/relationSubset")
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.map(item -> OBJECT_MAPPER.readValue(item, Relation.class))
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.count());
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Assertions
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.assertEquals(
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0, sc
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.textFile(workingDir.toString() + "/preparedInfo/resultSubset")
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.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class))
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.count());
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}
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@Test
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void matchTest() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/orcidtoresultfromsemrel/preparestep1")
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.getPath();
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PrepareResultOrcidAssociationStep1
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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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"-resultTableName", Publication.class.getCanonicalName(),
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"-outputPath", workingDir.toString() + "/preparedInfo",
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"-allowedsemrels", "IsSupplementedBy;IsSupplementTo",
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"-allowedpids", "orcid;orcid_pending"
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<ResultOrcidList> tmp = sc
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.textFile(workingDir.toString() + "/preparedInfo/publication")
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.map(item -> OBJECT_MAPPER.readValue(item, ResultOrcidList.class));
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Assertions.assertEquals(1, tmp.count());
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tmp.foreach(e -> System.out.println(OBJECT_MAPPER.writeValueAsString(e)));
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Assertions
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.assertEquals(
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1, tmp
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.filter(rol -> rol.getResultId().equals("50|475c1990cbb2::46b9f15a3e887ccb154a696c4e7e4217"))
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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(rol -> rol.getResultId().equals("50|475c1990cbb2::46b9f15a3e887ccb154a696c4e7e4217"))
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.collect()
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.get(0)
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.getAuthorList()
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.size());
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Assertions
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.assertEquals(
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"0000-0002-5001-6911",
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tmp
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.filter(rol -> rol.getResultId().equals("50|475c1990cbb2::46b9f15a3e887ccb154a696c4e7e4217"))
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.collect()
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.get(0)
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.getAuthorList()
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.get(0)
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.getOrcid());
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Assertions
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.assertEquals(
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"Barbarić-Mikočević, Željka",
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tmp
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.filter(rol -> rol.getResultId().equals("50|475c1990cbb2::46b9f15a3e887ccb154a696c4e7e4217"))
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.collect()
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.get(0)
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.getAuthorList()
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.get(0)
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.getFullname());
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Assertions
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.assertEquals(
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"Željka",
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tmp
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.filter(rol -> rol.getResultId().equals("50|475c1990cbb2::46b9f15a3e887ccb154a696c4e7e4217"))
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.collect()
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.get(0)
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.getAuthorList()
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.get(0)
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.getName());
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Assertions
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.assertEquals(
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"Barbarić-Mikočević",
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tmp
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.filter(rol -> rol.getResultId().equals("50|475c1990cbb2::46b9f15a3e887ccb154a696c4e7e4217"))
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.collect()
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.get(0)
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.getAuthorList()
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.get(0)
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.getSurname());
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Assertions
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.assertEquals(
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7, sc
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.textFile(workingDir.toString() + "/preparedInfo/relationSubset")
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.map(item -> OBJECT_MAPPER.readValue(item, Relation.class))
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.count());
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Assertions
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.assertEquals(
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1, sc
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.textFile(workingDir.toString() + "/preparedInfo/resultSubset")
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.map(item -> OBJECT_MAPPER.readValue(item, Publication.class))
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.count());
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}
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}
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