forked from D-Net/dnet-hadoop
test for propagation of result to community from organization and result to community from semrel
This commit is contained in:
parent
ec7f166690
commit
c925e2be16
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@ -1,4 +1,316 @@
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package eu.dnetlib.dhp.resulttocommunityfromorganization;
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package eu.dnetlib.dhp.resulttocommunityfromorganization;
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import static org.apache.spark.sql.functions.*;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.orcidtoresultfromsemrel.OrcidPropagationJobTest;
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import eu.dnetlib.dhp.schema.oaf.Dataset;
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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.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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public class ResultToCommunityJobTest {
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public class ResultToCommunityJobTest {
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private static final Logger log = LoggerFactory.getLogger(ResultToCommunityJobTest.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final ClassLoader cl = ResultToCommunityJobTest.class.getClassLoader();
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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(ResultToCommunityJobTest.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(ResultToCommunityJobTest.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 =
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SparkSession.builder()
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.appName(OrcidPropagationJobTest.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 test1() throws Exception {
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SparkResultToCommunityFromOrganizationJob2.main(
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new String[] {
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"-isTest",
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Boolean.TRUE.toString(),
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-sourcePath",
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getClass()
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.getResource("/eu/dnetlib/dhp/resulttocommunityfromorganization/sample")
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.getPath(),
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"-hive_metastore_uris",
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"",
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"-saveGraph",
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"true",
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"-resultTableName",
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"eu.dnetlib.dhp.schema.oaf.Dataset",
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"-outputPath",
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workingDir.toString() + "/dataset",
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"-preparedInfoPath",
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getClass()
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.getResource(
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"/eu/dnetlib/dhp/resulttocommunityfromorganization/preparedInfo")
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.getPath()
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});
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Dataset> tmp =
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sc.textFile(workingDir.toString() + "/dataset")
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.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
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Assertions.assertEquals(10, tmp.count());
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org.apache.spark.sql.Dataset<Dataset> verificationDataset =
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spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
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verificationDataset.createOrReplaceTempView("dataset");
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String query =
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"select id, MyT.id community "
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+ "from dataset "
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+ "lateral view explode(context) c as MyT "
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+ "lateral view explode(MyT.datainfo) d as MyD "
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+ "where MyD.inferenceprovenance = 'propagation'";
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org.apache.spark.sql.Dataset<Row> resultExplodedProvenance = spark.sql(query);
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Assertions.assertEquals(5, resultExplodedProvenance.count());
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Assertions.assertEquals(
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0,
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resultExplodedProvenance
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.filter("id = '50|dedup_wf_001::afaf128022d29872c4dad402b2db04fe'")
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.count());
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Assertions.assertEquals(
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1,
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resultExplodedProvenance
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.filter("id = '50|dedup_wf_001::3f62cfc27024d564ea86760c494ba93b'")
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.count());
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Assertions.assertEquals(
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"beopen",
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resultExplodedProvenance
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.select("community")
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.where(
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resultExplodedProvenance
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.col("id")
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.equalTo(
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"50|dedup_wf_001::3f62cfc27024d564ea86760c494ba93b"))
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.collectAsList()
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.get(0)
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.getString(0));
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Assertions.assertEquals(
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2,
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resultExplodedProvenance
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.filter("id = '50|od________18::8887b1df8b563c4ea851eb9c882c9d7b'")
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.count());
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Assertions.assertEquals(
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"mes",
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resultExplodedProvenance
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.select("community")
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.where(
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resultExplodedProvenance
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.col("id")
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.equalTo(
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"50|od________18::8887b1df8b563c4ea851eb9c882c9d7b"))
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.sort(desc("community"))
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.collectAsList()
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.get(0)
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.getString(0));
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Assertions.assertEquals(
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"euromarine",
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resultExplodedProvenance
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.select("community")
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.where(
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resultExplodedProvenance
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.col("id")
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.equalTo(
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"50|od________18::8887b1df8b563c4ea851eb9c882c9d7b"))
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.sort(desc("community"))
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.collectAsList()
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.get(1)
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.getString(0));
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Assertions.assertEquals(
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1,
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resultExplodedProvenance
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.filter("id = '50|doajarticles::8d817039a63710fcf97e30f14662c6c8'")
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.count());
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Assertions.assertEquals(
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"mes",
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resultExplodedProvenance
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.select("community")
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.where(
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resultExplodedProvenance
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.col("id")
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.equalTo(
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"50|doajarticles::8d817039a63710fcf97e30f14662c6c8"))
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.sort(desc("community"))
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.collectAsList()
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.get(0)
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.getString(0));
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Assertions.assertEquals(
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1,
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resultExplodedProvenance
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.filter("id = '50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6'")
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.count());
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Assertions.assertEquals(
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"mes",
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resultExplodedProvenance
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.select("community")
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.where(
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resultExplodedProvenance
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.col("id")
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.equalTo(
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"50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6"))
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.sort(desc("community"))
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.collectAsList()
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.get(0)
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.getString(0));
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/*
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{"communityList":["euromarine","mes"],"resultId":"50|doajarticles::8d817039a63710fcf97e30f14662c6c8"} "context" ["id": euromarine] updates = 1
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{"communityList":["euromarine","mes"],"resultId":"50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6"} context = [ni, euromarine] updates = 1
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*/
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query =
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"select id, MyT.id community "
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+ "from dataset "
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+ "lateral view explode(context) c as MyT "
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+ "lateral view explode(MyT.datainfo) d as MyD ";
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org.apache.spark.sql.Dataset<Row> resultCommunityId = spark.sql(query);
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Assertions.assertEquals(10, resultCommunityId.count());
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Assertions.assertEquals(
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1,
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resultCommunityId
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.filter("id = '50|dedup_wf_001::afaf128022d29872c4dad402b2db04fe'")
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.count());
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Assertions.assertEquals(
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"beopen",
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resultCommunityId
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.select("community")
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.where(
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resultCommunityId
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.col("id")
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.equalTo(
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"50|dedup_wf_001::afaf128022d29872c4dad402b2db04fe"))
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.collectAsList()
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.get(0)
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.getString(0));
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Assertions.assertEquals(
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1,
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resultCommunityId
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.filter("id = '50|dedup_wf_001::3f62cfc27024d564ea86760c494ba93b'")
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.count());
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Assertions.assertEquals(
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3,
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resultCommunityId
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.filter("id = '50|od________18::8887b1df8b563c4ea851eb9c882c9d7b'")
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.count());
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Assertions.assertEquals(
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"beopen",
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resultCommunityId
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.select("community")
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.where(
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resultCommunityId
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.col("id")
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.equalTo(
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"50|od________18::8887b1df8b563c4ea851eb9c882c9d7b"))
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.sort(desc("community"))
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.collectAsList()
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.get(2)
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.getString(0));
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Assertions.assertEquals(
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2,
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resultCommunityId
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.filter("id = '50|doajarticles::8d817039a63710fcf97e30f14662c6c8'")
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.count());
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Assertions.assertEquals(
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"euromarine",
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resultCommunityId
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.select("community")
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.where(
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resultCommunityId
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.col("id")
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.equalTo(
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"50|doajarticles::8d817039a63710fcf97e30f14662c6c8"))
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.sort(desc("community"))
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.collectAsList()
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.get(1)
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.getString(0));
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Assertions.assertEquals(
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3,
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resultCommunityId
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.filter("id = '50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6'")
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.count());
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Assertions.assertEquals(
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"euromarine",
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resultCommunityId
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.select("community")
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.where(
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resultCommunityId
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.col("id")
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.equalTo(
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"50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6"))
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.sort(desc("community"))
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.collectAsList()
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.get(2)
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.getString(0));
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Assertions.assertEquals(
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"ni",
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resultCommunityId
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.select("community")
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.where(
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resultCommunityId
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.col("id")
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.equalTo(
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"50|doajarticles::3c98f0632f1875b4979e552ba3aa01e6"))
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.sort(desc("community"))
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.collectAsList()
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.get(0)
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.getString(0));
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}
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}
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}
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@ -1,4 +1,280 @@
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package eu.dnetlib.dhp.resulttocommunityfromsemrel;
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package eu.dnetlib.dhp.resulttocommunityfromsemrel;
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import static org.apache.spark.sql.functions.desc;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.orcidtoresultfromsemrel.OrcidPropagationJobTest;
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import eu.dnetlib.dhp.schema.oaf.Dataset;
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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.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.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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public class ResultToCommunityJobTest {
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public class ResultToCommunityJobTest {
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private static final Logger log =
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LoggerFactory.getLogger(
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eu.dnetlib.dhp.resulttocommunityfromsemrel.ResultToCommunityJobTest.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final ClassLoader cl =
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eu.dnetlib.dhp.resulttocommunityfromsemrel.ResultToCommunityJobTest.class
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.getClassLoader();
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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 =
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Files.createTempDirectory(
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eu.dnetlib.dhp.resulttocommunityfromsemrel.ResultToCommunityJobTest.class
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.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(
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eu.dnetlib.dhp.resulttocommunityfromsemrel.ResultToCommunityJobTest.class
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.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 =
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SparkSession.builder()
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.appName(OrcidPropagationJobTest.class.getSimpleName())
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||||||
|
.config(conf)
|
||||||
|
.getOrCreate();
|
||||||
|
}
|
||||||
|
|
||||||
|
@AfterAll
|
||||||
|
public static void afterAll() throws IOException {
|
||||||
|
FileUtils.deleteDirectory(workingDir.toFile());
|
||||||
|
spark.stop();
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
public void test1() throws Exception {
|
||||||
|
SparkResultToCommunityThroughSemRelJob4.main(
|
||||||
|
new String[] {
|
||||||
|
"-isTest", Boolean.TRUE.toString(),
|
||||||
|
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||||
|
"-sourcePath",
|
||||||
|
getClass()
|
||||||
|
.getResource(
|
||||||
|
"/eu/dnetlib/dhp/resulttocommunityfromsemrel/sample")
|
||||||
|
.getPath(),
|
||||||
|
"-hive_metastore_uris", "",
|
||||||
|
"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Dataset",
|
||||||
|
"-outputPath", workingDir.toString() + "/dataset",
|
||||||
|
"-preparedInfoPath",
|
||||||
|
getClass()
|
||||||
|
.getResource(
|
||||||
|
"/eu/dnetlib/dhp/resulttocommunityfromsemrel/preparedInfo")
|
||||||
|
.getPath()
|
||||||
|
});
|
||||||
|
|
||||||
|
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||||
|
|
||||||
|
JavaRDD<Dataset> tmp =
|
||||||
|
sc.textFile(workingDir.toString() + "/dataset")
|
||||||
|
.map(item -> OBJECT_MAPPER.readValue(item, Dataset.class));
|
||||||
|
|
||||||
|
Assertions.assertEquals(10, tmp.count());
|
||||||
|
org.apache.spark.sql.Dataset<Dataset> verificationDataset =
|
||||||
|
spark.createDataset(tmp.rdd(), Encoders.bean(Dataset.class));
|
||||||
|
|
||||||
|
verificationDataset.createOrReplaceTempView("dataset");
|
||||||
|
|
||||||
|
String query =
|
||||||
|
"select id, MyT.id community "
|
||||||
|
+ "from dataset "
|
||||||
|
+ "lateral view explode(context) c as MyT "
|
||||||
|
+ "lateral view explode(MyT.datainfo) d as MyD "
|
||||||
|
+ "where MyD.inferenceprovenance = 'propagation'";
|
||||||
|
|
||||||
|
org.apache.spark.sql.Dataset<Row> resultExplodedProvenance = spark.sql(query);
|
||||||
|
Assertions.assertEquals(5, resultExplodedProvenance.count());
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
0,
|
||||||
|
resultExplodedProvenance
|
||||||
|
.filter("id = '50|dedup_wf_001::2305908abeca9da37eaf3bddcaf81b7b'")
|
||||||
|
.count());
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
1,
|
||||||
|
resultExplodedProvenance
|
||||||
|
.filter("id = '50|dedup_wf_001::0489ae524201eedaa775da282dce35e7'")
|
||||||
|
.count());
|
||||||
|
Assertions.assertEquals(
|
||||||
|
"dh-ch",
|
||||||
|
resultExplodedProvenance
|
||||||
|
.select("community")
|
||||||
|
.where(
|
||||||
|
resultExplodedProvenance
|
||||||
|
.col("id")
|
||||||
|
.equalTo(
|
||||||
|
"50|dedup_wf_001::0489ae524201eedaa775da282dce35e7"))
|
||||||
|
.collectAsList()
|
||||||
|
.get(0)
|
||||||
|
.getString(0));
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
3,
|
||||||
|
resultExplodedProvenance
|
||||||
|
.filter("id = '50|dedup_wf_001::0a60e33b4f0986ebd9819451f2d87a28'")
|
||||||
|
.count());
|
||||||
|
List<Row> rowList =
|
||||||
|
resultExplodedProvenance
|
||||||
|
.select("community")
|
||||||
|
.where(
|
||||||
|
resultExplodedProvenance
|
||||||
|
.col("id")
|
||||||
|
.equalTo(
|
||||||
|
"50|dedup_wf_001::0a60e33b4f0986ebd9819451f2d87a28"))
|
||||||
|
.sort(desc("community"))
|
||||||
|
.collectAsList();
|
||||||
|
Assertions.assertEquals("mes", rowList.get(0).getString(0));
|
||||||
|
Assertions.assertEquals("fam", rowList.get(1).getString(0));
|
||||||
|
Assertions.assertEquals("ee", rowList.get(2).getString(0));
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
1,
|
||||||
|
resultExplodedProvenance
|
||||||
|
.filter("id = '50|dedup_wf_001::0ae02edb5598a5545d10b107fcf48dcc'")
|
||||||
|
.count());
|
||||||
|
Assertions.assertEquals(
|
||||||
|
"aginfra",
|
||||||
|
resultExplodedProvenance
|
||||||
|
.select("community")
|
||||||
|
.where(
|
||||||
|
resultExplodedProvenance
|
||||||
|
.col("id")
|
||||||
|
.equalTo(
|
||||||
|
"50|dedup_wf_001::0ae02edb5598a5545d10b107fcf48dcc"))
|
||||||
|
.collectAsList()
|
||||||
|
.get(0)
|
||||||
|
.getString(0));
|
||||||
|
|
||||||
|
query =
|
||||||
|
"select id, MyT.id community "
|
||||||
|
+ "from dataset "
|
||||||
|
+ "lateral view explode(context) c as MyT "
|
||||||
|
+ "lateral view explode(MyT.datainfo) d as MyD ";
|
||||||
|
|
||||||
|
org.apache.spark.sql.Dataset<Row> resultCommunityId = spark.sql(query);
|
||||||
|
|
||||||
|
Assertions.assertEquals(10, resultCommunityId.count());
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
2,
|
||||||
|
resultCommunityId
|
||||||
|
.filter("id = '50|dedup_wf_001::0489ae524201eedaa775da282dce35e7'")
|
||||||
|
.count());
|
||||||
|
rowList =
|
||||||
|
resultCommunityId
|
||||||
|
.select("community")
|
||||||
|
.where(
|
||||||
|
resultCommunityId
|
||||||
|
.col("id")
|
||||||
|
.equalTo(
|
||||||
|
"50|dedup_wf_001::0489ae524201eedaa775da282dce35e7"))
|
||||||
|
.sort(desc("community"))
|
||||||
|
.collectAsList();
|
||||||
|
Assertions.assertEquals("dh-ch", rowList.get(0).getString(0));
|
||||||
|
Assertions.assertEquals("beopen", rowList.get(1).getString(0));
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
3,
|
||||||
|
resultCommunityId
|
||||||
|
.filter("id = '50|dedup_wf_001::0a60e33b4f0986ebd9819451f2d87a28'")
|
||||||
|
.count());
|
||||||
|
rowList =
|
||||||
|
resultCommunityId
|
||||||
|
.select("community")
|
||||||
|
.where(
|
||||||
|
resultCommunityId
|
||||||
|
.col("id")
|
||||||
|
.equalTo(
|
||||||
|
"50|dedup_wf_001::0a60e33b4f0986ebd9819451f2d87a28"))
|
||||||
|
.sort(desc("community"))
|
||||||
|
.collectAsList();
|
||||||
|
Assertions.assertEquals("mes", rowList.get(0).getString(0));
|
||||||
|
Assertions.assertEquals("fam", rowList.get(1).getString(0));
|
||||||
|
Assertions.assertEquals("ee", rowList.get(2).getString(0));
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
2,
|
||||||
|
resultCommunityId
|
||||||
|
.filter("id = '50|dedup_wf_001::0ae02edb5598a5545d10b107fcf48dcc'")
|
||||||
|
.count());
|
||||||
|
rowList =
|
||||||
|
resultCommunityId
|
||||||
|
.select("community")
|
||||||
|
.where(
|
||||||
|
resultCommunityId
|
||||||
|
.col("id")
|
||||||
|
.equalTo(
|
||||||
|
"50|dedup_wf_001::0ae02edb5598a5545d10b107fcf48dcc"))
|
||||||
|
.sort(desc("community"))
|
||||||
|
.collectAsList();
|
||||||
|
Assertions.assertEquals("beopen", rowList.get(0).getString(0));
|
||||||
|
Assertions.assertEquals("aginfra", rowList.get(1).getString(0));
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
2,
|
||||||
|
resultCommunityId
|
||||||
|
.filter("id = '50|dedup_wf_001::2305908abeca9da37eaf3bddcaf81b7b'")
|
||||||
|
.count());
|
||||||
|
rowList =
|
||||||
|
resultCommunityId
|
||||||
|
.select("community")
|
||||||
|
.where(
|
||||||
|
resultCommunityId
|
||||||
|
.col("id")
|
||||||
|
.equalTo(
|
||||||
|
"50|dedup_wf_001::2305908abeca9da37eaf3bddcaf81b7b"))
|
||||||
|
.sort(desc("community"))
|
||||||
|
.collectAsList();
|
||||||
|
Assertions.assertEquals("euromarine", rowList.get(1).getString(0));
|
||||||
|
Assertions.assertEquals("ni", rowList.get(0).getString(0));
|
||||||
|
|
||||||
|
Assertions.assertEquals(
|
||||||
|
1,
|
||||||
|
resultCommunityId
|
||||||
|
.filter("id = '50|doajarticles::8d817039a63710fcf97e30f14662c6c8'")
|
||||||
|
.count());
|
||||||
|
Assertions.assertEquals(
|
||||||
|
"euromarine",
|
||||||
|
resultCommunityId
|
||||||
|
.select("community")
|
||||||
|
.where(
|
||||||
|
resultCommunityId
|
||||||
|
.col("id")
|
||||||
|
.equalTo(
|
||||||
|
"50|doajarticles::8d817039a63710fcf97e30f14662c6c8"))
|
||||||
|
.collectAsList()
|
||||||
|
.get(0)
|
||||||
|
.getString(0));
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue