forked from D-Net/dnet-hadoop
refactoring
This commit is contained in:
parent
1a89f8211c
commit
124591a7f3
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@ -26,7 +26,6 @@ public class Constants {
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public static String ORCID = "orcid";
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static {
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accessRightsCoarMap.put("OPEN", "c_abf2");
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accessRightsCoarMap.put("RESTRICTED", "c_16ec");
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@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.*;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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@ -20,6 +19,7 @@ import eu.dnetlib.dhp.oa.graph.dump.Constants;
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import eu.dnetlib.dhp.oa.graph.dump.ResultMapper;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
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import eu.dnetlib.dhp.schema.dump.oaf.community.Project;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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@ -6,7 +6,6 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.Optional;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.MapFunction;
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@ -21,6 +20,7 @@ import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.Constants;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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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.Result;
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import scala.Tuple2;
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@ -164,7 +164,7 @@ public class CreateEntityTest {
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final Consumer<ContextInfo> consumer = ci -> cInfoList.add(ci);
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queryInformationSystem.getContextInformation(consumer);
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for(ContextInfo cInfo: cInfoList){
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for (ContextInfo cInfo : cInfoList) {
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writer.write(new Gson().toJson(Process.getEntity(cInfo)));
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}
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writer.close();
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@ -1,9 +1,11 @@
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package eu.dnetlib.dhp.oa.graph.dump.funderresult;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Result;
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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 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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@ -17,117 +19,119 @@ 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 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 com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Result;
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public class ResultLinkedToProjectTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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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 SparkSession spark;
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private static Path workingDir;
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private static Path workingDir;
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private static final Logger log = LoggerFactory
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.getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class);
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private static final Logger log = LoggerFactory
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.getLogger(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class);
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private static HashMap<String, String> map = new HashMap<>();
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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(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName());
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log.info("using work dir {}", workingDir);
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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(
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eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.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(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName());
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SparkConf conf = new SparkConf();
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conf.setAppName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.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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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(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.class.getSimpleName())
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.config(conf)
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.getOrCreate();
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}
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spark = SparkSession
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.builder()
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.appName(eu.dnetlib.dhp.oa.graph.dump.funderresult.ResultLinkedToProjectTest.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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@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 testNoMatch() throws Exception {
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@Test
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public void testNoMatch() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json")
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.getPath();
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json")
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.getPath();
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final String relationPath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json")
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.getPath();
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final String relationPath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json")
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.getPath();
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SparkResultLinkedToProject.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/preparedInfo",
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"-sourcePath", sourcePath,
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-relationPath", relationPath
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SparkResultLinkedToProject.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/preparedInfo",
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"-sourcePath", sourcePath,
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-relationPath", relationPath
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});
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Result> tmp = sc
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.textFile(workingDir.toString() + "/preparedInfo")
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.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
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JavaRDD<Result> tmp = sc
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.textFile(workingDir.toString() + "/preparedInfo")
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.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
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org.apache.spark.sql.Dataset<Result> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Result.class));
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org.apache.spark.sql.Dataset<Result> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Result.class));
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Assertions.assertEquals(0, verificationDataset.count());
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Assertions.assertEquals(0, verificationDataset.count());
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}
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}
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@Test
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public void testMatchOne() throws Exception {
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@Test
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public void testMatchOne() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json")
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.getPath();
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/papers.json")
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.getPath();
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final String relationPath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json")
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.getPath();
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final String relationPath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json")
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.getPath();
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SparkResultLinkedToProject.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/preparedInfo",
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"-sourcePath", sourcePath,
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-relationPath", relationPath
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SparkResultLinkedToProject.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/preparedInfo",
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"-sourcePath", sourcePath,
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"-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication",
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"-relationPath", relationPath
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});
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});
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<Publication> tmp = sc
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.textFile(workingDir.toString() + "/preparedInfo")
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.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
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JavaRDD<Publication> tmp = sc
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.textFile(workingDir.toString() + "/preparedInfo")
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.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
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org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
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org.apache.spark.sql.Dataset<Publication> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(Publication.class));
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Assertions.assertEquals(1, verificationDataset.count());
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Assertions.assertEquals(1, verificationDataset.count());
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}
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}
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}
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@ -1,11 +1,10 @@
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package eu.dnetlib.dhp.oa.graph.dump.funderresult;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
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import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit;
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import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults;
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import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
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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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@ -19,124 +18,124 @@ 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 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 com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest;
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import eu.dnetlib.dhp.oa.graph.dump.SplitForCommunityTest;
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import eu.dnetlib.dhp.oa.graph.dump.community.CommunitySplit;
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import eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults;
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import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult;
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public class SplitPerFunderTest {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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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 SparkSession spark;
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private static Path workingDir;
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private static Path workingDir;
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private static final Logger log = LoggerFactory.getLogger(SplitPerFunderTest.class);
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private static final Logger log = LoggerFactory.getLogger(SplitPerFunderTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(SplitPerFunderTest.class.getSimpleName());
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log.info("using work dir {}", workingDir);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(SplitPerFunderTest.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(SplitPerFunderTest.class.getSimpleName());
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SparkConf conf = new SparkConf();
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conf.setAppName(SplitPerFunderTest.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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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(SplitPerFunderTest.class.getSimpleName())
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.config(conf)
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.getOrCreate();
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}
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spark = SparkSession
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.builder()
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.appName(SplitPerFunderTest.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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@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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@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/funderresource/extendeddump")
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.getPath();
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/extendeddump")
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.getPath();
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SparkDumpFunderResults.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/split",
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"-sourcePath", sourcePath,
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"-relationPath", sourcePath
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});
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SparkDumpFunderResults.main(new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-outputPath", workingDir.toString() + "/split",
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"-sourcePath", sourcePath,
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"-relationPath", sourcePath
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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});
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// FP7 3
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JavaRDD<CommunityResult> tmp = sc
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.textFile(workingDir.toString() + "/split/EC_FP7")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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Assertions.assertEquals(3, verificationDataset.count());
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// FP7 3
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JavaRDD<CommunityResult> tmp = sc
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.textFile(workingDir.toString() + "/split/EC_FP7")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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Assertions
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.assertEquals(
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1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count());
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org.apache.spark.sql.Dataset<CommunityResult> verificationDataset = spark
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.createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class));
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// CIHR 2
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tmp = sc
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.textFile(workingDir.toString() + "/split/CIHR")
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.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
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Assertions.assertEquals(2, tmp.count());
|
||||
|
||||
Assertions.assertEquals(3, verificationDataset.count());
|
||||
// NWO 1
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/NWO")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(1, tmp.count());
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
1, verificationDataset.filter("id = '50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776'").count());
|
||||
// NIH 3
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/NIH")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(2, tmp.count());
|
||||
|
||||
// NSF 1
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/NSF")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(1, tmp.count());
|
||||
|
||||
// CIHR 2
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/CIHR")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(2, tmp.count());
|
||||
// SNSF 1
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/SNSF")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(1, tmp.count());
|
||||
|
||||
//NWO 1
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/NWO")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(1, tmp.count());
|
||||
// NHMRC 1
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/NHMRC")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(1, tmp.count());
|
||||
|
||||
//NIH 3
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/NIH")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(2, tmp.count());
|
||||
// H2020 3
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/EC_H2020")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(3, tmp.count());
|
||||
|
||||
//NSF 1
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/NSF")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(1, tmp.count());
|
||||
|
||||
//SNSF 1
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/SNSF")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(1, tmp.count());
|
||||
|
||||
//NHMRC 1
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/NHMRC")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(1, tmp.count());
|
||||
|
||||
//H2020 3
|
||||
tmp = sc
|
||||
.textFile(workingDir.toString() + "/split/EC_H2020")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class));
|
||||
Assertions.assertEquals(3, tmp.count());
|
||||
|
||||
}
|
||||
}
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue