[DUMP CSV] test and resources for the SelectResultAndDumpRelation job
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package eu.dnetlib.dhp.oa.graph.dump.csv;
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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.HashMap;
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import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVRELCommunityResult;
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import eu.dnetlib.dhp.utils.DHPUtils;
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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.api.java.function.ForeachFunction;
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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.oa.graph.dump.complete.SelectRelationTest;
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import eu.dnetlib.dhp.oa.graph.dump.complete.SparkSelectValidRelationsJob;
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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 11/05/23
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*/
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public class SelectResultAndDumpRelationTest {
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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(SelectResultAndDumpRelationTest.class);
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private static HashMap<String, String> map = new HashMap<>();
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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(SelectResultAndDumpRelationTest.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(SelectResultAndDumpRelationTest.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(SelectResultAndDumpRelationTest.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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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/csv/input/")
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.getPath();
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SparkSelectResultsAndDumpRelations.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/output",
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"-workingPath", workingDir.toString() + "/working",
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"-communities", "enermaps;dh-ch",
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"-sourcePath", sourcePath
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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Assertions.assertEquals(2,sc.textFile(workingDir.toString() + "/working/communityResultIds").count());
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Assertions.assertEquals(1, sc.textFile(workingDir.toString() + "/working/communityResultIds")
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.filter(v -> v.equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")).count());
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Assertions.assertEquals(1, sc.textFile(workingDir.toString() + "/working/communityResultIds")
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.filter(v -> v.equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).count());
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//verify that the association is correct with the communityid and result id
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spark.read().option("header", "true").option("delimiter",Constants.SEP).csv(workingDir.toString() + "/output/result_community")
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.createOrReplaceTempView("result_community");
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Assertions.assertEquals(3, spark.sql("SELECT * FROM result_community").count());
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Assertions.assertEquals(1, spark.sql("SELECT * " +
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"FROM result_community " +
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"WHERE community_id = '" + DHPUtils.md5("dh-ch") + "'").count());
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Assertions.assertEquals(1, spark.sql("SELECT * " +
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"FROM result_community" +
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" WHERE result_id = '50|DansKnawCris::0224aae28af558f21768dbc6439c7a95' " +
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"AND community_id = '" + DHPUtils.md5("dh-ch") + "'").count());
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Assertions.assertEquals(2, spark.sql("SELECT * " +
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"FROM result_community " +
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"WHERE community_id = '" + DHPUtils.md5("enermaps") + "'").count());
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Assertions.assertEquals(1, spark.sql("SELECT * " +
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"FROM result_community " +
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"WHERE result_id = '50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9' " +
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"AND community_id = '" + DHPUtils.md5("enermaps") + "'").count());
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Assertions.assertEquals(1, spark.sql("SELECT * " +
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"FROM result_community " +
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"WHERE result_id = '50|DansKnawCris::0224aae28af558f21768dbc6439c7a95' " +
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"AND community_id = '" + DHPUtils.md5("enermaps") + "'").count());
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Assertions.assertEquals(3, spark.read().textFile(workingDir.toString() + "/working/resultIds").count());
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Assertions.assertEquals(1, sc.textFile(workingDir.toString() + "/working/resultIds")
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.filter(v -> v.equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")).count());
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Assertions.assertEquals(1, sc.textFile(workingDir.toString() + "/working/resultIds")
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.filter(v -> v.equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")).count());
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Assertions.assertEquals(1, sc.textFile(workingDir.toString() + "/working/resultIds")
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.filter(v -> v.equals("50|DansKnawCris::26780065282e607306372abd0d808245")).count());
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spark.read().option("header", "true").option("delimiter",Constants.SEP).csv(workingDir.toString() + "/output/relation")
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.createOrReplaceTempView("relation");
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Assertions.assertEquals(2, spark.sql("SELECT * FROM relation").count());
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Assertions.assertEquals(1, spark.sql("SELECT * FROM relation WHERE id = '" +
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DHPUtils.md5(("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9cites50|DansKnawCris::26780065282e607306372abd0d808245")) + "'").count());
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Assertions.assertEquals(1, spark.sql("SELECT * FROM relation WHERE id = '" +
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DHPUtils.md5(("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9cites50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) + "'").count());
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}
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}
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{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"isProvidedBy","relType":"datasourceOrganization","source":"10|doajarticles::2baa9032dc058d3c8ff780c426b0c19f","subRelType":"provision","target":"20|dedup_wf_001::2899e571609779168222fdeb59cb916d"}
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{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"Cites","relType":"datasourceOrganization","source":"50|DansKnawCris::26780065282e607306372abd0d808245","subRelType":"provision","target":"50|DansKnawCris::26780065282e607306372abd0d808246"}
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{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"Cites","relType":"datasourceOrganization","source":"50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9","subRelType":"provision","target":"50|DansKnawCris::26780065282e607306372abd0d808245"}
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{"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"lastupdatetimestamp":1592688952862,"properties":[],"relClass":"Cites","relType":"datasourceOrganization","source":"50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9","subRelType":"provision","target":"50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"}
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