[Clean Country] first implementation to remove country NL from results collected from NARCIS when doi starts with mendely prefix
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package eu.dnetlib.dhp.oa.graph.clean;
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/**
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* @author miriam.baglioni
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* @Date 20/07/22
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*/
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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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.FilterFunction;
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import org.apache.spark.api.java.function.MapFunction;
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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.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.io.Serializable;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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public class CleanCountrySparkJob implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(CleanCountrySparkJob.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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CleanContextSparkJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/input_clean_country_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputPath = parser.get("inputPath");
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log.info("inputPath: {}", inputPath);
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String workingPath = parser.get("workingPath");
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log.info("workingPath: {}", workingPath);
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String country = parser.get("country");
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log.info("country: {}", country);
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String verifyParam = parser.get("verifyParam");
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log.info("verifyParam: {}", verifyParam);
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String collectedfrom = parser.get("collectedfrom");
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log.info("collectedfrom: {}", collectedfrom);
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String graphTableClassName = parser.get("graphTableClassName");
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log.info("graphTableClassName: {}", graphTableClassName);
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Class<? extends Result> entityClazz = (Class<? extends Result>) Class.forName(graphTableClassName);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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cleanCountry(spark, country, verifyParam, inputPath, entityClazz, workingPath,collectedfrom);
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});
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}
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private static <T extends Result> void cleanCountry(SparkSession spark, String country, String verifyParam,
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String inputPath, Class<T> entityClazz, String workingPath, String collectedfrom) {
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Dataset<T> res = spark
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.read()
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.textFile(inputPath)
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.map(
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(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
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Encoders.bean(entityClazz))
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;
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res.map((MapFunction<T, T>) r -> {
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for(StructuredProperty p: r.getPid()){
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if (p.getQualifier().getClassid().equalsIgnoreCase("doi") &&
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p.getValue().startsWith(verifyParam) && r.getCollectedfrom().stream().anyMatch(cf -> cf.getValue().equalsIgnoreCase(collectedfrom))) {
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r
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.setCountry(
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r
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.getCountry()
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.stream()
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.filter(
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c -> !c.getClassid()
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.equalsIgnoreCase(country))
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.collect(Collectors.toList()));
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}
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}
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return r;
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}, Encoders.bean(entityClazz))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(workingPath);
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spark
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.read()
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.textFile(workingPath)
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.map(
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(MapFunction<String, T>) value -> OBJECT_MAPPER.readValue(value, entityClazz),
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Encoders.bean(entityClazz))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(inputPath);
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}
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}
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@ -0,0 +1,43 @@
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[
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{
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"paramName": "issm",
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"paramLongName": "isSparkSessionManaged",
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"paramDescription": "when true will stop SparkSession after job execution",
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"paramRequired": false
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},
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{
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"paramName": "in",
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"paramLongName": "inputPath",
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"paramDescription": "the path to the graph data dump to read",
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"paramRequired": true
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},
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{
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"paramName": "wp",
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"paramLongName": "workingPath",
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"paramDescription": "the path to store the output graph",
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"paramRequired": true
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},
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{
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"paramName": "c",
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"paramLongName": "country",
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"paramDescription": "the id of the context to be removed",
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"paramRequired": true
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},
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{
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"paramName": "class",
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"paramLongName": "graphTableClassName",
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"paramDescription": "class name moelling the graph table",
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"paramRequired": true
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},{
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"paramName": "vf",
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"paramLongName": "verifyParam",
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"paramDescription": "the parameter to be verified to remove the country",
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"paramRequired": true
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},
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{
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"paramName": "cf",
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"paramLongName": "collectedfrom",
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"paramDescription": "the collectedfrom value for which we should apply the cleaning",
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"paramRequired": true
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}
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]
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@ -0,0 +1,135 @@
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package eu.dnetlib.dhp.oa.graph.clean;
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/**
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* @author miriam.baglioni
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* @Date 20/07/22
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*/
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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.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.StructuredProperty;
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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.MapFunction;
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import org.apache.spark.sql.Encoders;
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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 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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public class CleanCountryTest {
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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.getLogger(CleanContextTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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workingDir = Files.createTempDirectory(DumpJobTest.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(DumpJobTest.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(DumpJobTest.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 testResultClean() throws Exception {
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final String sourcePath = getClass()
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.getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_country.json")
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.getPath();
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final String prefix = "gcube ";
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spark
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.read()
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.textFile(sourcePath)
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.map(
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(MapFunction<String, Publication>) r -> OBJECT_MAPPER.readValue(r, Publication.class),
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Encoders.bean(Publication.class))
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.write()
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.json(workingDir.toString() + "/publication");
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CleanCountrySparkJob.main(new String[] {
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"--isSparkSessionManaged", Boolean.FALSE.toString(),
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"--inputPath", workingDir.toString() + "/publication",
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"-graphTableClassName", Publication.class.getCanonicalName(),
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"-workingPath", workingDir.toString() + "/working",
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"-country", "NL",
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"-verifyParam", "10.17632",
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"-collectedfrom", "NARCIS"
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});
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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() + "/publication")
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.map(item -> OBJECT_MAPPER.readValue(item, Publication.class));
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Assertions.assertEquals(7, tmp.count());
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// original result with NL country and doi starting with Mendely prefix, but not collectedfrom NARCIS
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Assertions
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.assertEquals(
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1,
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tmp
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.filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95"))
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.collect()
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.get(0)
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.getCountry()
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.size());
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// original result with NL country and pid not starting with Mendely prefix
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Assertions
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.assertEquals(
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1,
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tmp
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.filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9"))
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.collect()
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.get(0)
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.getCountry()
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.size());
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// original result with NL country and doi starting with Mendely prefix and collectedfrom NARCIS
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Assertions
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.assertEquals(
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0,
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tmp
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.filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af"))
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.collect()
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.get(0)
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.getCountry()
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.size());
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}
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}
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