[OpenCitation] change the integration logic to consider dois with commas inside
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1f8302dc37
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fbc28ee8c3
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package eu.dnetlib.dhp.actionmanager.opencitations;
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import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER;
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import static eu.dnetlib.dhp.actionmanager.Constants.isSparkSessionManaged;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.IOException;
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import java.io.Serializable;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.LocatedFileStatus;
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import org.apache.hadoop.fs.Path;
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import org.apache.hadoop.fs.RemoteIterator;
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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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import org.apache.spark.sql.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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public class ReadCOCI implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(ReadCOCI.class);
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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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ReadCOCI.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/opencitations/input_readcoci_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final String hdfsNameNode = parser.get("nameNode");
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log.info("nameNode: {}", hdfsNameNode);
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final String inputPath = parser.get("sourcePath");
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log.info("input path : {}", inputPath);
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Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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Configuration conf = new Configuration();
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conf.set("fs.defaultFS", hdfsNameNode);
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FileSystem fileSystem = FileSystem.get(conf);
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SparkConf sconf = new SparkConf();
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final String delimiter = Optional
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.ofNullable(parser.get("delimiter"))
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.orElse(DEFAULT_DELIMITER);
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runWithSparkSession(
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sconf,
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isSparkSessionManaged,
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spark -> {
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doRead(
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spark,
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fileSystem,
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inputPath,
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outputPath,
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delimiter);
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});
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}
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public static void doRead(SparkSession spark, FileSystem fileSystem, String inputPath, String outputPath,
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String delimiter) throws IOException {
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RemoteIterator<LocatedFileStatus> iterator = fileSystem
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.listFiles(
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new Path(inputPath), true);
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while (iterator.hasNext()) {
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LocatedFileStatus fileStatus = iterator.next();
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Path p = fileStatus.getPath();
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String p_string = p.toString();
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Dataset<Row> cociData = spark
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.read()
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.format("csv")
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.option("sep", delimiter)
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.option("inferSchema", "true")
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.option("header", "true")
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.option("quotes", "\"")
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.load(p_string);
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cociData.map((MapFunction<Row, COCI>) row -> {
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COCI coci = new COCI();
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coci.setOci(row.getString(0));
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coci.setCiting(row.getString(1));
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coci.setCited(row.getString(2));
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return coci;
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}, Encoders.bean(COCI.class))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath + "/" + p_string.substring(p_string.lastIndexOf("/") + 1));
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}
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}
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}
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@ -0,0 +1,89 @@
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package eu.dnetlib.dhp.actionmanager.opencitations.model;
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import java.io.Serializable;
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import com.opencsv.bean.CsvBindByPosition;
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public class COCI implements Serializable {
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@CsvBindByPosition(position = 0)
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// @CsvBindByName(column = "doi")
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private String oci;
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@CsvBindByPosition(position = 1)
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// @CsvBindByName(column = "level1")
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private String citing;
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@CsvBindByPosition(position = 2)
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// @CsvBindByName(column = "level2")
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private String cited;
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@CsvBindByPosition(position = 3)
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// @CsvBindByName(column = "level3")
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private String creation;
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@CsvBindByPosition(position = 4)
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private String timespan;
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@CsvBindByPosition(position = 5)
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private String journal_sc;
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@CsvBindByPosition(position = 6)
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private String author_sc;
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public String getOci() {
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return oci;
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}
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public void setOci(String oci) {
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this.oci = oci;
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}
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public String getCiting() {
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return citing;
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}
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public void setCiting(String citing) {
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this.citing = citing;
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}
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public String getCited() {
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return cited;
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}
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public void setCited(String cited) {
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this.cited = cited;
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}
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public String getCreation() {
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return creation;
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}
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public void setCreation(String creation) {
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this.creation = creation;
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}
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public String getTimespan() {
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return timespan;
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}
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public void setTimespan(String timespan) {
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this.timespan = timespan;
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}
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public String getJournal_sc() {
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return journal_sc;
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}
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public void setJournal_sc(String journal_sc) {
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this.journal_sc = journal_sc;
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}
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public String getAuthor_sc() {
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return author_sc;
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}
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public void setAuthor_sc(String author_sc) {
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this.author_sc = author_sc;
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}
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}
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@ -0,0 +1,36 @@
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[
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{
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"paramName": "sp",
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"paramLongName": "sourcePath",
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"paramDescription": "the zipped opencitations file",
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"paramRequired": true
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},
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{
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"paramName": "nn",
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"paramLongName": "nameNode",
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"paramDescription": "the hdfs name node",
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"paramRequired": true
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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": "the hdfs name node",
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"paramRequired": false
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},
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{
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"paramName": "d",
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"paramLongName": "delimiter",
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"paramDescription": "the hdfs name node",
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"paramRequired": false
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},
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{
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"paramName": "op",
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"paramLongName": "outputPath",
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"paramDescription": "the hdfs name node",
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"paramRequired": false
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}
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]
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@ -0,0 +1,94 @@
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package eu.dnetlib.dhp.actionmanager.opencitations;
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import static eu.dnetlib.dhp.actionmanager.Constants.DEFAULT_DELIMITER;
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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.hadoop.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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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.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.actionmanager.opencitations.model.COCI;
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import eu.dnetlib.dhp.schema.oaf.Dataset;
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public class ReadCOCITest {
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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(ReadCOCITest.class);
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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(ReadCOCITest.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(ReadCOCITest.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(ReadCOCITest.class.getSimpleName())
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.config(conf)
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.getOrCreate();
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}
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@AfterAll
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public static void afterAll() throws IOException {
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FileUtils.deleteDirectory(workingDir.toFile());
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spark.stop();
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}
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@Test
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void testReadCOCI() throws Exception {
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String inputPath = getClass()
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.getResource(
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"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
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.getPath();
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ReadCOCI
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.doRead(
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spark, FileSystem.getLocal(new Configuration()), inputPath,
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workingDir.toString() + "/COCI", DEFAULT_DELIMITER);
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<COCI> tmp = sc
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.textFile(workingDir.toString() + "/COCI/*/")
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.map(item -> OBJECT_MAPPER.readValue(item, COCI.class));
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Assertions.assertEquals(23, tmp.count());
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Assertions.assertEquals(1, tmp.filter(c -> c.getCiting().equals("10.1207/s15327647jcd3,4-01")).count());
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Assertions.assertEquals(8, tmp.filter(c -> c.getCiting().indexOf(".refs") > -1).count());
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}
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}
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oci,citing,cited,creation,timespan,journal_sc,author_sc
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0200102000736280105030207060407191213036204630001-02001000107362800030005000000090000000006060903,"10.1207/s15327647jcd3,4-01",10.1017/s0305000900006693,2002-11-01,P17Y1M,no,no
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