forked from D-Net/dnet-hadoop
[OCNEW] added creation of the actionset for the results classified with FoS based ont he OpenAIRE identifier
This commit is contained in:
parent
3cd5590f3b
commit
7827a2d66b
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@ -75,6 +75,7 @@ public class GetFOSSparkJob implements Serializable {
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fosData.map((MapFunction<Row, FOSDataModel>) r -> {
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FOSDataModel fosDataModel = new FOSDataModel();
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fosDataModel.setDoi(r.getString(0).toLowerCase());
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fosDataModel.setOaid(r.getString(1).toLowerCase());
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fosDataModel.setLevel1(r.getString(2));
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fosDataModel.setLevel2(r.getString(3));
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fosDataModel.setLevel3(r.getString(4));
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@ -16,12 +16,14 @@ 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.jetbrains.annotations.NotNull;
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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.createunresolvedentities.model.FOSDataModel;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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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 eu.dnetlib.dhp.schema.oaf.Subject;
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@ -52,62 +54,90 @@ public class PrepareFOSSparkJob implements Serializable {
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final Boolean distributeDOI = Optional
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.ofNullable(parser.get("distributeDoi"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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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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distributeFOSdois(
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spark,
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sourcePath,
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if (distributeDOI)
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distributeFOSdois(
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spark,
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sourcePath,
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outputPath);
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outputPath);
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else
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distributeFOSoaid(spark, sourcePath, outputPath);
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});
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}
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private static void distributeFOSoaid(SparkSession spark, String sourcePath, String outputPath) {
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Dataset<FOSDataModel> fosDataset = readPath(spark, sourcePath, FOSDataModel.class);
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fosDataset
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.groupByKey((MapFunction<FOSDataModel, String>) v -> v.getOaid().toLowerCase(), Encoders.STRING())
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.mapGroups((MapGroupsFunction<String, FOSDataModel, Result>) (k, it) -> {
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return getResult(ModelSupport.getIdPrefix(Result.class) + "|" + k, it);
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}, Encoders.bean(Result.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 + "/fos");
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}
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@NotNull
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private static Result getResult(String k, Iterator<FOSDataModel> it) {
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Result r = new Result();
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FOSDataModel first = it.next();
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r.setId(k);
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HashSet<String> level1 = new HashSet<>();
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HashSet<String> level2 = new HashSet<>();
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HashSet<String> level3 = new HashSet<>();
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HashSet<String> level4 = new HashSet<>();
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addLevels(level1, level2, level3, level4, first);
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it.forEachRemaining(v -> addLevels(level1, level2, level3, level4, v));
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List<Subject> sbjs = new ArrayList<>();
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level1
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.forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
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level2
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.forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
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level3
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.forEach(
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l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true)));
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level4
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.forEach(
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l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true)));
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r.setSubject(sbjs);
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r
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.setDataInfo(
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OafMapperUtils
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.dataInfo(
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false, null, true,
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false,
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OafMapperUtils
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.qualifier(
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ModelConstants.PROVENANCE_ENRICH,
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null,
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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ModelConstants.DNET_PROVENANCE_ACTIONS),
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null));
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return r;
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}
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private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) {
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Dataset<FOSDataModel> fosDataset = readPath(spark, sourcePath, FOSDataModel.class);
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fosDataset
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.groupByKey((MapFunction<FOSDataModel, String>) v -> v.getDoi().toLowerCase(), Encoders.STRING())
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.mapGroups((MapGroupsFunction<String, FOSDataModel, Result>) (k, it) -> {
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Result r = new Result();
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FOSDataModel first = it.next();
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r.setId(DHPUtils.generateUnresolvedIdentifier(k, DOI));
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HashSet<String> level1 = new HashSet<>();
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HashSet<String> level2 = new HashSet<>();
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HashSet<String> level3 = new HashSet<>();
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HashSet<String> level4 = new HashSet<>();
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addLevels(level1, level2, level3, level4, first);
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it.forEachRemaining(v -> addLevels(level1, level2, level3, level4, v));
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List<Subject> sbjs = new ArrayList<>();
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level1
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.forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
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level2
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.forEach(l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID)));
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level3
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.forEach(
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l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true)));
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level4
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.forEach(
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l -> add(sbjs, getSubject(l, FOS_CLASS_ID, FOS_CLASS_NAME, UPDATE_SUBJECT_FOS_CLASS_ID, true)));
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r.setSubject(sbjs);
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r
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.setDataInfo(
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OafMapperUtils
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.dataInfo(
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false, null, true,
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false,
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OafMapperUtils
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.qualifier(
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ModelConstants.PROVENANCE_ENRICH,
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null,
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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ModelConstants.DNET_PROVENANCE_ACTIONS),
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null));
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return r;
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}, Encoders.bean(Result.class))
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.mapGroups(
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(MapGroupsFunction<String, FOSDataModel, Result>) (k,
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it) -> getResult(DHPUtils.generateUnresolvedIdentifier(k, DOI), it),
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Encoders.bean(Result.class))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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@ -0,0 +1,92 @@
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package eu.dnetlib.dhp.actionmanager.fosnodoi;
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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.*;
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import org.apache.commons.cli.ParseException;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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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.JavaPairRDD;
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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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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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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.Result;
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import eu.dnetlib.dhp.schema.oaf.utils.*;
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import scala.Tuple2;
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public class CreateActionSetSparkJob implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(final String[] args) throws IOException, ParseException {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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Objects
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.requireNonNull(
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CreateActionSetSparkJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/fosnodoi/as_parameters.json"))));
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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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final String inputPath = parser.get("sourcePath");
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log.info("inputPath {}", inputPath);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}", outputPath);
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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 -> createActionSet(spark, inputPath, outputPath));
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}
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private static void createActionSet(SparkSession spark, String inputPath, String outputPath) {
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spark
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.read()
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.textFile(inputPath)
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.map(
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(MapFunction<String, Result>) value -> OBJECT_MAPPER.readValue(value, Result.class),
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Encoders.bean(Result.class))
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.toJavaRDD()
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.map(p -> new AtomicAction(p.getClass(), p))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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.saveAsHadoopFile(
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outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
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}
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}
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@ -16,5 +16,10 @@
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"paramLongName": "outputPath",
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"paramDescription": "the path of the new ActionSet",
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"paramRequired": true
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}
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}, {
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"paramName": "fd",
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"paramLongName": "distributeDoi",
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"paramDescription": "the path of the new ActionSet",
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"paramRequired": false
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}
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]
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@ -0,0 +1,20 @@
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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": "op",
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"paramLongName": "outputPath",
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"paramDescription": "the working path",
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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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@ -0,0 +1,30 @@
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<configuration>
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<property>
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<name>jobTracker</name>
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<value>yarnRM</value>
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</property>
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<property>
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<name>nameNode</name>
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<value>hdfs://nameservice1</value>
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</property>
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<property>
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<name>oozie.use.system.libpath</name>
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<value>true</value>
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</property>
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<property>
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<name>hiveMetastoreUris</name>
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<value>thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083</value>
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</property>
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<property>
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<name>hiveJdbcUrl</name>
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<value>jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000</value>
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</property>
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<property>
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<name>hiveDbName</name>
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<value>openaire</value>
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</property>
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<property>
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<name>oozie.launcher.mapreduce.user.classpath.first</name>
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<value>true</value>
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</property>
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</configuration>
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@ -0,0 +1,153 @@
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<workflow-app name="FOS no doi" xmlns="uri:oozie:workflow:0.5">
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<parameters>
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<property>
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<name>fosPath</name>
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<description>the input path of the resources to be extended</description>
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</property>
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<property>
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<name>outputPath</name>
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<description>the path where to store the actionset</description>
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</property>
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<property>
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<name>sparkDriverMemory</name>
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<description>memory for driver process</description>
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</property>
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<property>
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<name>sparkExecutorMemory</name>
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<description>memory for individual executor</description>
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</property>
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<property>
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<name>sparkExecutorCores</name>
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<description>number of cores used by single executor</description>
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</property>
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<property>
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<name>oozieActionShareLibForSpark2</name>
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<description>oozie action sharelib for spark 2.*</description>
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</property>
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<property>
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<name>spark2ExtraListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorAppListener</value>
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<description>spark 2.* extra listeners classname</description>
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</property>
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<property>
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<name>spark2SqlQueryExecutionListeners</name>
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<value>com.cloudera.spark.lineage.NavigatorQueryListener</value>
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<description>spark 2.* sql query execution listeners classname</description>
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</property>
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<property>
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<name>spark2YarnHistoryServerAddress</name>
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<description>spark 2.* yarn history server address</description>
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</property>
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<property>
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<name>spark2EventLogDir</name>
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<description>spark 2.* event log dir location</description>
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</property>
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</parameters>
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<global>
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<job-tracker>${jobTracker}</job-tracker>
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<name-node>${nameNode}</name-node>
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<configuration>
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<property>
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<name>mapreduce.job.queuename</name>
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<value>${queueName}</value>
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</property>
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<property>
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<name>oozie.launcher.mapred.job.queue.name</name>
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<value>${oozieLauncherQueueName}</value>
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</property>
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<property>
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<name>oozie.action.sharelib.for.spark</name>
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<value>${oozieActionShareLibForSpark2}</value>
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</property>
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</configuration>
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</global>
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<start to="getFOS"/>
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<kill name="Kill">
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<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
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</kill>
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<action name="getFOS">
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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>Gets Data from FOS csv file</name>
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<class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSSparkJob</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>${fosPath}</arg>
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<arg>--outputPath</arg><arg>${workingDir}/input/fos</arg>
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<arg>--delimiter</arg><arg>${delimiter}</arg>
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</spark>
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<ok to="prepareFos"/>
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<error to="Kill"/>
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</action>
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<action name="prepareFos">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<mode>cluster</mode>
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<name>Produces the results from FOS</name>
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<class>eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareFOSSparkJob</class>
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<jar>dhp-aggregation-${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=${sparkSqlWarehouseDir}
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</spark-opts>
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<arg>--sourcePath</arg><arg>${workingDir}/input/fos</arg>
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<arg>--outputPath</arg><arg>${workingDir}/prepared</arg>
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<arg>--distributeDoi</arg><arg>false</arg>
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</spark>
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<ok to="produceActionSet"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
|
||||
|
||||
<action name="produceActionSet">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Save the action set grouping results with the same id</name>
|
||||
<class>eu.dnetlib.dhp.actionmanager.fosnodoi.CreateActionSetSparkJob</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
--driver-memory=${sparkDriverMemory}
|
||||
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--sourcePath</arg><arg>${workingDir}/prepared/fos</arg>
|
||||
<arg>--outputPath</arg><arg>${outputPath}</arg>
|
||||
</spark>
|
||||
<ok to="End"/>
|
||||
<error to="Kill"/>
|
||||
</action>
|
||||
|
||||
<end name="End"/>
|
||||
</workflow-app>
|
||||
|
|
@ -0,0 +1,176 @@
|
|||
|
||||
package eu.dnetlib.dhp.actionmanager.fosnodoi;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.hadoop.io.Text;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.Dataset;
|
||||
import org.apache.spark.sql.Encoders;
|
||||
import org.apache.spark.sql.Row;
|
||||
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.schema.action.AtomicAction;
|
||||
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
||||
|
||||
public class CreateActionSetSparkJobTest {
|
||||
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
private static SparkSession spark;
|
||||
|
||||
private static Path workingDir;
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJobTest.class);
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files
|
||||
.createTempDirectory(CreateActionSetSparkJobTest.class.getSimpleName());
|
||||
log.info("using work dir {}", workingDir);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(CreateActionSetSparkJobTest.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(CreateActionSetSparkJobTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
|
||||
private void runJob(String resultsInputPath, String outputPath) throws Exception {
|
||||
CreateActionSetSparkJob
|
||||
.main(
|
||||
new String[] {
|
||||
"-isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"-sourcePath", resultsInputPath,
|
||||
|
||||
"-outputPath", outputPath,
|
||||
});
|
||||
}
|
||||
|
||||
@Test
|
||||
void testScores() throws Exception {
|
||||
|
||||
String resultsInputPath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/actionmanager/fosnodoi/results.json")
|
||||
.getPath();
|
||||
|
||||
String outputPath = workingDir.toString() + "/actionSet";
|
||||
|
||||
// execute the job to generate the action sets for result scores
|
||||
runJob(resultsInputPath, outputPath);
|
||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
||||
|
||||
sc
|
||||
.sequenceFile(outputPath, Text.class, Text.class)
|
||||
.foreach(t -> System.out.println(new ObjectMapper().writeValueAsString(t)));
|
||||
|
||||
}
|
||||
|
||||
void assertResultImpactScores(Dataset<Row> testDataset) {
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"6.63451994567e-09", testDataset
|
||||
.filter(
|
||||
"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
|
||||
"and id = 'influence'")
|
||||
.select("value")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(0));
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"0.348694533145", testDataset
|
||||
.filter(
|
||||
"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
|
||||
"and id = 'popularity_alt'")
|
||||
.select("value")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(0));
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"2.16094680115e-09", testDataset
|
||||
.filter(
|
||||
"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
|
||||
"and id = 'popularity'")
|
||||
.select("value")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(0));
|
||||
}
|
||||
|
||||
void assertProjectImpactScores(Dataset<Row> testDataset) throws Exception {
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"0", testDataset
|
||||
.filter(
|
||||
"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
|
||||
"and id = 'numOfInfluentialResults'")
|
||||
.select("value")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(0));
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"1", testDataset
|
||||
.filter(
|
||||
"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
|
||||
"and id = 'numOfPopularResults'")
|
||||
.select("value")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(0));
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"25", testDataset
|
||||
.filter(
|
||||
"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
|
||||
"and id = 'totalImpulse'")
|
||||
.select("value")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(0));
|
||||
Assertions
|
||||
.assertEquals(
|
||||
"43", testDataset
|
||||
.filter(
|
||||
"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
|
||||
"and id = 'totalCitationCount'")
|
||||
.select("value")
|
||||
.collectAsList()
|
||||
.get(0)
|
||||
.getString(0));
|
||||
}
|
||||
}
|
||||
|
|
@ -0,0 +1,104 @@
|
|||
|
||||
package eu.dnetlib.dhp.actionmanager.fosnodoi;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.LocalFileSystem;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
import org.apache.spark.sql.SparkSession;
|
||||
import org.junit.jupiter.api.*;
|
||||
import org.slf4j.Logger;
|
||||
import org.slf4j.LoggerFactory;
|
||||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSSparkJob;
|
||||
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareTest;
|
||||
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.ProduceTest;
|
||||
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel;
|
||||
|
||||
/**
|
||||
* @author miriam.baglioni
|
||||
* @Date 13/02/23
|
||||
*/
|
||||
public class GetFosTest {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(ProduceTest.class);
|
||||
|
||||
private static Path workingDir;
|
||||
private static SparkSession spark;
|
||||
private static LocalFileSystem fs;
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files.createTempDirectory(PrepareTest.class.getSimpleName());
|
||||
|
||||
fs = FileSystem.getLocal(new Configuration());
|
||||
log.info("using work dir {}", workingDir);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(ProduceTest.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(PrepareTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
|
||||
@Test
|
||||
@Disabled
|
||||
void test3() throws Exception {
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.csv")
|
||||
.getPath();
|
||||
|
||||
final String outputPath = workingDir.toString() + "/fos.json";
|
||||
GetFOSSparkJob
|
||||
.main(
|
||||
new String[] {
|
||||
"--isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"--sourcePath", sourcePath,
|
||||
|
||||
"-outputPath", outputPath,
|
||||
"-delimiter", ","
|
||||
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<FOSDataModel> tmp = sc
|
||||
.textFile(outputPath)
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, FOSDataModel.class));
|
||||
|
||||
tmp.foreach(t -> Assertions.assertTrue(t.getOaid() != null));
|
||||
tmp.foreach(t -> Assertions.assertTrue(t.getLevel1() != null));
|
||||
tmp.foreach(t -> Assertions.assertTrue(t.getLevel2() != null));
|
||||
tmp.foreach(t -> Assertions.assertTrue(t.getLevel3() != null));
|
||||
|
||||
tmp.foreach(t -> System.out.println(new ObjectMapper().writeValueAsString(t)));
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,99 @@
|
|||
|
||||
package eu.dnetlib.dhp.actionmanager.fosnodoi;
|
||||
|
||||
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||
import static org.junit.jupiter.api.Assertions.assertTrue;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.nio.file.Files;
|
||||
import java.nio.file.Path;
|
||||
|
||||
import org.apache.commons.io.FileUtils;
|
||||
import org.apache.hadoop.conf.Configuration;
|
||||
import org.apache.hadoop.fs.FileSystem;
|
||||
import org.apache.hadoop.fs.LocalFileSystem;
|
||||
import org.apache.spark.SparkConf;
|
||||
import org.apache.spark.api.java.JavaRDD;
|
||||
import org.apache.spark.api.java.JavaSparkContext;
|
||||
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.createunresolvedentities.PrepareFOSSparkJob;
|
||||
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareSDGSparkJob;
|
||||
import eu.dnetlib.dhp.actionmanager.createunresolvedentities.ProduceTest;
|
||||
import eu.dnetlib.dhp.schema.oaf.Result;
|
||||
|
||||
public class PrepareTest {
|
||||
|
||||
private static final Logger log = LoggerFactory.getLogger(ProduceTest.class);
|
||||
|
||||
private static Path workingDir;
|
||||
private static SparkSession spark;
|
||||
private static LocalFileSystem fs;
|
||||
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||
|
||||
@BeforeAll
|
||||
public static void beforeAll() throws IOException {
|
||||
workingDir = Files.createTempDirectory(PrepareTest.class.getSimpleName());
|
||||
|
||||
fs = FileSystem.getLocal(new Configuration());
|
||||
log.info("using work dir {}", workingDir);
|
||||
|
||||
SparkConf conf = new SparkConf();
|
||||
conf.setAppName(ProduceTest.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(PrepareTest.class.getSimpleName())
|
||||
.config(conf)
|
||||
.getOrCreate();
|
||||
}
|
||||
|
||||
@AfterAll
|
||||
public static void afterAll() throws IOException {
|
||||
FileUtils.deleteDirectory(workingDir.toFile());
|
||||
spark.stop();
|
||||
}
|
||||
|
||||
@Test
|
||||
void fosPrepareTest() throws Exception {
|
||||
final String sourcePath = getClass()
|
||||
.getResource("/eu/dnetlib/dhp/actionmanager/fosnodoi/fosnodoi.json")
|
||||
.getPath();
|
||||
|
||||
PrepareFOSSparkJob
|
||||
.main(
|
||||
new String[] {
|
||||
"--isSparkSessionManaged", Boolean.FALSE.toString(),
|
||||
"--sourcePath", sourcePath,
|
||||
|
||||
"-outputPath", workingDir.toString() + "/work",
|
||||
"-distributeDoi", Boolean.FALSE.toString()
|
||||
|
||||
});
|
||||
|
||||
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
||||
|
||||
JavaRDD<Result> tmp = sc
|
||||
.textFile(workingDir.toString() + "/work/fos")
|
||||
.map(item -> OBJECT_MAPPER.readValue(item, Result.class));
|
||||
|
||||
tmp.foreach(t -> System.out.println(new ObjectMapper().writeValueAsString(t)));
|
||||
|
||||
}
|
||||
|
||||
}
|
||||
|
|
@ -0,0 +1,19 @@
|
|||
DOI,OAID,level1,level2,level3,level4,score_for_L3,score_for_L4
|
||||
N/A,78975075580c::e680668c98366c9cd6349afc62486a7f,03 medical and health sciences,0301 basic medicine,030104 developmental biology,N/A,0.5,0.0
|
||||
N/A,78975075580c::e680668c98366c9cd6349afc62486a7f,03 medical and health sciences,0303 health sciences,030304 developmental biology,N/A,0.5,0.0
|
||||
N/A,od______2806::a1da9d2678b12969a9ab5f50b5e71d0a,05 social sciences,0501 psychology and cognitive sciences,050109 social psychology,05010904 Group processes/Collective identity,0.5589094161987305,0.5166763067245483
|
||||
N/A,od______2806::a1da9d2678b12969a9ab5f50b5e71d0a,05 social sciences,0501 psychology and cognitive sciences,050105 experimental psychology,05010501 Emotion/Affective science,0.44109055399894714,0.4833236634731293
|
||||
N/A,doajarticles::76535d77fd2a5fe9810aefafffb8ef6c,05 social sciences,0502 economics and business,050203 business & management,05020302 Supply chain management/Business terms,0.5459638833999634,0.5460261106491089
|
||||
N/A,doajarticles::76535d77fd2a5fe9810aefafffb8ef6c,05 social sciences,0502 economics and business,050211 marketing,05021102 Services marketing/Retailing,0.4540362060070038,0.4539738595485687
|
||||
N/A,od_______156::a3a0119c6d9d3a66943f8da042e97a5e,01 natural sciences,0105 earth and related environmental sciences,010504 meteorology & atmospheric sciences,01050407 Geomagnetism/Ionosphere,0.5131047964096069,0.4990350902080536
|
||||
N/A,od_______156::a3a0119c6d9d3a66943f8da042e97a5e,01 natural sciences,0105 earth and related environmental sciences,010502 geochemistry & geophysics,01050203 Seismology/Seismology measurement,0.4868951737880707,0.500964879989624
|
||||
N/A,od______2806::4b9a664dd6b8b04204cb613e7bc9c873,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis,03022002 Medical imaging/Medical physics,0.5068133473396301,0.10231181626910052
|
||||
N/A,od______2806::4b9a664dd6b8b04204cb613e7bc9c873,03 medical and health sciences,0302 clinical medicine,030204 cardiovascular system & hematology,N/A,0.49318668246269226,0.0
|
||||
N/A,od______3341::ef754de29464abf9bc9b99664630ce74,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis,03022012 Oncology/Infectious causes of cancer,0.5,0.5
|
||||
N/A,od______3341::ef754de29464abf9bc9b99664630ce74,03 medical and health sciences,0302 clinical medicine,030220 oncology & carcinogenesis,03022012 Oncology/Infectious causes of cancer,0.5,0.5
|
||||
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Reference in New Issue