[OpenCitation] change the integration logic to consider dois with commas inside
This commit is contained in:
parent
1f8302dc37
commit
fbc28ee8c3
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@ -14,6 +14,7 @@ import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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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.FlatMapFunction;
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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.slf4j.Logger;
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@ -21,6 +22,7 @@ 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.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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@ -83,10 +85,16 @@ public class CreateActionSetSparkJob implements Serializable {
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private static void extractContent(SparkSession spark, String inputPath, String outputPath,
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boolean shouldDuplicateRels) {
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spark
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.sqlContext()
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.createDataset(spark.sparkContext().textFile(inputPath + "/*", 6000), Encoders.STRING())
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.read()
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.textFile(inputPath + "/*")
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.map(
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(MapFunction<String, COCI>) value -> OBJECT_MAPPER.readValue(value, COCI.class),
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Encoders.bean(COCI.class))
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// spark
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// .sqlContext()
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// .createDataset(spark.sparkContext().textFile(inputPath + "/*", 6000), Encoders.STRING())
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.flatMap(
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(FlatMapFunction<String, Relation>) value -> createRelation(value, shouldDuplicateRels).iterator(),
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(FlatMapFunction<COCI, Relation>) value -> createRelation(value, shouldDuplicateRels).iterator(),
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Encoders.bean(Relation.class))
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.filter((FilterFunction<Relation>) value -> value != null)
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.toJavaRDD()
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@ -98,15 +106,14 @@ public class CreateActionSetSparkJob implements Serializable {
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}
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private static List<Relation> createRelation(String value, boolean duplicate) {
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String[] line = value.split(",");
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if (!line[1].startsWith("10.")) {
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return new ArrayList<>();
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}
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private static List<Relation> createRelation(COCI value, boolean duplicate) {
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List<Relation> relationList = new ArrayList<>();
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String citing = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[1]));
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final String cited = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[2]));
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String citing = ID_PREFIX
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCiting()));
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final String cited = ID_PREFIX
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+ IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", value.getCited()));
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relationList
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.addAll(
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@ -114,9 +121,11 @@ public class CreateActionSetSparkJob implements Serializable {
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citing,
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cited));
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if (duplicate && line[1].endsWith(".refs")) {
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if (duplicate && value.getCiting().endsWith(".refs")) {
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citing = ID_PREFIX + IdentifierFactory
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.md5(CleaningFunctions.normalizePidValue("doi", line[1].substring(0, line[1].indexOf(".refs"))));
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.md5(
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CleaningFunctions
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.normalizePidValue("doi", value.getCiting().substring(0, value.getCiting().indexOf(".refs"))));
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relationList.addAll(getRelations(citing, cited));
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}
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@ -0,0 +1,111 @@
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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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@ -26,6 +26,7 @@
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<switch>
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<case to="download">${wf:conf('resumeFrom') eq 'DownloadDump'}</case>
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<case to="extract">${wf:conf('resumeFrom') eq 'ExtractContent'}</case>
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<case to="read">${wf:conf('resumeFrom') eq 'ReadContent'}</case>
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<default to="create_actionset"/> <!-- first action to be done when downloadDump is to be performed -->
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</switch>
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</decision>
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@ -60,6 +61,32 @@
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<arg>--inputFile</arg><arg>${inputFile}</arg>
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<arg>--workingPath</arg><arg>${workingPath}</arg>
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</java>
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<ok to="read"/>
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<error to="Kill"/>
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</action>
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<action name="read">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Produces the AS for OC</name>
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<class>eu.dnetlib.dhp.actionmanager.opencitations.ReadCOCI</class>
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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
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--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${workingPath}/COCI</arg>
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<arg>--outputPath</arg><arg>${workingDir}/COCI</arg>
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<arg>--nameNode</arg><arg>${nameNode}</arg>
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<arg>--delimiter</arg><arg>${delimiter}</arg>
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</spark>
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<ok to="create_actionset"/>
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<error to="Kill"/>
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</action>
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@ -76,7 +76,7 @@ public class CreateOpenCitationsASTest {
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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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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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.getPath();
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CreateActionSetSparkJob
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@ -99,7 +99,7 @@ public class CreateOpenCitationsASTest {
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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.map(aa -> ((Relation) aa.getPayload()));
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assertEquals(60, tmp.count());
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assertEquals(62, tmp.count());
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// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
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@ -110,7 +110,7 @@ public class CreateOpenCitationsASTest {
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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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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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.getPath();
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CreateActionSetSparkJob
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@ -131,7 +131,7 @@ public class CreateOpenCitationsASTest {
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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.map(aa -> ((Relation) aa.getPayload()));
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assertEquals(44, tmp.count());
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assertEquals(46, tmp.count());
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// tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r)));
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@ -142,7 +142,7 @@ public class CreateOpenCitationsASTest {
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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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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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.getPath();
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CreateActionSetSparkJob
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@ -175,7 +175,7 @@ public class CreateOpenCitationsASTest {
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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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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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.getPath();
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CreateActionSetSparkJob
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@ -215,7 +215,7 @@ public class CreateOpenCitationsASTest {
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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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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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.getPath();
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CreateActionSetSparkJob
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@ -240,8 +240,8 @@ public class CreateOpenCitationsASTest {
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assertEquals("citation", r.getSubRelType());
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assertEquals("resultResult", r.getRelType());
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});
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assertEquals(22, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
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assertEquals(22, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
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assertEquals(23, tmp.filter(r -> r.getRelClass().equals("Cites")).count());
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assertEquals(23, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count());
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}
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@ -250,7 +250,7 @@ public class CreateOpenCitationsASTest {
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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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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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.getPath();
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CreateActionSetSparkJob
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@ -295,7 +295,7 @@ public class CreateOpenCitationsASTest {
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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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"/eu/dnetlib/dhp/actionmanager/opencitations/COCI")
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.getPath();
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CreateActionSetSparkJob
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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;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.AfterAll;
|
||||
import org.junit.jupiter.api.Assertions;
|
||||
import org.junit.jupiter.api.BeforeAll;
|
||||
import org.junit.jupiter.api.Test;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.actionmanager.opencitations.model.COCI;
|
||||
import eu.dnetlib.dhp.schema.oaf.Dataset;
|
||||
|
||||
public class ReadCOCITest {
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
private static SparkSession spark;
|
||||
|
||||
private static Path workingDir;
|
||||
private static final Logger log = LoggerFactory
|
||||
.getLogger(ReadCOCITest.class);
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files
|
||||
.createTempDirectory(ReadCOCITest.class.getSimpleName());
|
||||
log.info("using work dir {}", workingDir);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(ReadCOCITest.class.getSimpleName());
|
||||
|
||||
conf.setMaster("local[*]");
|
||||
conf.set("spark.driver.host", "localhost");
|
||||
conf.set("hive.metastore.local", "true");
|
||||
conf.set("spark.ui.enabled", "false");
|
||||
conf.set("spark.sql.warehouse.dir", workingDir.toString());
|
||||
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
|
||||
|
||||
spark = SparkSession
|
||||
.builder()
|
||||
.appName(ReadCOCITest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
|
||||
@Test
|
||||
void testReadCOCI() throws Exception {
|
||||
String inputPath = getClass()
|
||||
.getResource(
|
||||
"/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles")
|
||||
.getPath();
|
||||
|
||||
ReadCOCI
|
||||
.doRead(
|
||||
spark, FileSystem.getLocal(new Configuration()), inputPath,
|
||||
workingDir.toString() + "/COCI", DEFAULT_DELIMITER);
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<COCI> tmp = sc
|
||||
.textFile(workingDir.toString() + "/COCI/*/")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, COCI.class));
|
||||
|
||||
Assertions.assertEquals(23, tmp.count());
|
||||
|
||||
Assertions.assertEquals(1, tmp.filter(c -> c.getCiting().equals("10.1207/s15327647jcd3,4-01")).count());
|
||||
|
||||
Assertions.assertEquals(8, tmp.filter(c -> c.getCiting().indexOf(".refs") > -1).count());
|
||||
}
|
||||
|
||||
}
|
||||
Binary file not shown.
Binary file not shown.
Binary file not shown.
Binary file not shown.
|
|
@ -0,0 +1,2 @@
|
|||
oci,citing,cited,creation,timespan,journal_sc,author_sc
|
||||
0200102000736280105030207060407191213036204630001-02001000107362800030005000000090000000006060903,"10.1207/s15327647jcd3,4-01",10.1017/s0305000900006693,2002-11-01,P17Y1M,no,no
|
||||
|
|
@ -348,9 +348,9 @@ public abstract class AbstractMdRecordToOafMapper {
|
|||
r.setContext(prepareContexts(doc, info));
|
||||
r.setExternalReference(new ArrayList<>()); // NOT PRESENT IN MDSTORES
|
||||
r
|
||||
.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
|
||||
.setProcessingchargeamount(field(doc.valueOf("//oaf:processingchargeamount"), info));
|
||||
r
|
||||
.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
|
||||
.setProcessingchargecurrency(field(doc.valueOf("//oaf:processingchargeamount/@currency"), info));
|
||||
|
||||
r.setInstance(instances);
|
||||
r.setBestaccessright(OafMapperUtils.createBestAccessRights(instances));
|
||||
|
|
|
|||
|
|
@ -44,7 +44,7 @@
|
|||
<pluginRepository>
|
||||
<id>iis-releases</id>
|
||||
<name>iis releases plugin repository</name>
|
||||
<url>http://maven.ceon.pl/artifactory/iis-releases</url>
|
||||
<url>https://maven.ceon.pl/artifactory/iis-releases</url>
|
||||
<layout>default</layout>
|
||||
</pluginRepository>
|
||||
</pluginRepositories>
|
||||
|
|
|
|||
Loading…
Reference in New Issue