forked from D-Net/dnet-hadoop
Fixes in workflow.xml
This commit is contained in:
Serafeim Chatzopoulos
parent
db4ca43ee8
commit
2cc5b1a39b
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@ -9,7 +9,6 @@ import java.util.List;
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import java.util.Optional;
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import java.util.stream.Collectors;
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import eu.dnetlib.dhp.actionmanager.bipmodel.score.deserializers.BipProjectModel;
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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.mapred.SequenceFileOutputFormat;
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@ -25,8 +24,9 @@ import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.bipmodel.score.deserializers.BipResultModel;
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import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
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import eu.dnetlib.dhp.actionmanager.bipmodel.score.deserializers.BipProjectModel;
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import eu.dnetlib.dhp.actionmanager.bipmodel.score.deserializers.BipResultModel;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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@ -89,8 +89,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
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default:
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throw new RuntimeException("Unknown target entity: " + targetEntity);
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}
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}
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);
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});
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}
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private static <I extends Project> void prepareProjects(SparkSession spark, String inputPath, String outputPath) {
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@ -98,7 +97,7 @@ public class SparkAtomicActionScoreJob implements Serializable {
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// read input bip project scores
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Dataset<BipProjectModel> projectScores = readPath(spark, inputPath, BipProjectModel.class);
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projectScores.map( (MapFunction<BipProjectModel, Project>) bipProjectScores -> {
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projectScores.map((MapFunction<BipProjectModel, Project>) bipProjectScores -> {
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Project project = new Project();
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project.setId(bipProjectScores.getProjectId());
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project.setMeasures(bipProjectScores.toMeasures());
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@ -106,7 +105,8 @@ public class SparkAtomicActionScoreJob implements Serializable {
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}, Encoders.bean(Project.class))
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.toJavaRDD()
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.map(p -> new AtomicAction(Project.class, p))
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.mapToPair( aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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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(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
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@ -1,21 +1,23 @@
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package eu.dnetlib.dhp.actionmanager.bipmodel.score.deserializers;
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import com.opencsv.bean.CsvBindByPosition;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import lombok.AllArgsConstructor;
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import lombok.Getter;
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import lombok.NoArgsConstructor;
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import lombok.Setter;
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import eu.dnetlib.dhp.schema.oaf.Measure;
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import static eu.dnetlib.dhp.actionmanager.Constants.*;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.Collections;
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import java.util.List;
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import static eu.dnetlib.dhp.actionmanager.Constants.*;
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import com.opencsv.bean.CsvBindByPosition;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Measure;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import lombok.AllArgsConstructor;
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import lombok.Getter;
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import lombok.NoArgsConstructor;
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import lombok.Setter;
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@NoArgsConstructor
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@AllArgsConstructor
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@ -38,32 +40,35 @@ public class BipProjectModel {
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KeyValue kv = new KeyValue();
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kv.setKey("score");
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kv.setValue(measureValue);
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kv.setDataInfo(
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OafMapperUtils.dataInfo(
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kv
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.setDataInfo(
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OafMapperUtils
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.dataInfo(
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false,
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UPDATE_DATA_INFO_TYPE,
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true,
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false,
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OafMapperUtils.qualifier(
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OafMapperUtils
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.qualifier(
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UPDATE_MEASURE_BIP_CLASS_ID,
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UPDATE_CLASS_NAME,
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ModelConstants.DNET_PROVENANCE_ACTIONS,
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ModelConstants.DNET_PROVENANCE_ACTIONS),
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"")
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);
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""));
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Measure measure = new Measure();
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measure.setId(measureId);
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measure.setUnit(Collections.singletonList(kv));
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return measure;
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}
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public List<Measure> toMeasures() {
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return Arrays.asList(
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return Arrays
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.asList(
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createMeasure("numOfInfluentialResults", numOfInfluentialResults),
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createMeasure("numOfPopularResults", numOfPopularResults),
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createMeasure("totalImpulse", totalImpulse),
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createMeasure("totalCitationCount", totalCitationCount)
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);
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createMeasure("totalCitationCount", totalCitationCount));
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}
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}
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@ -1,13 +1,13 @@
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package eu.dnetlib.dhp.actionmanager.bipmodel.score.deserializers;
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import eu.dnetlib.dhp.actionmanager.bipmodel.Score;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.HashMap;
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import java.util.List;
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import eu.dnetlib.dhp.actionmanager.bipmodel.Score;
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/**
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* Class that maps the model of the bipFinder! input data.
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* Only needed for deserialization purposes
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@ -24,8 +24,8 @@ import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.bipmodel.score.deserializers.BipResultModel;
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import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
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import eu.dnetlib.dhp.actionmanager.bipmodel.score.deserializers.BipResultModel;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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@ -7,8 +7,6 @@ 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 eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Project;
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import org.apache.commons.io.FileUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.spark.SparkConf;
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@ -28,6 +26,8 @@ import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Project;
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import eu.dnetlib.dhp.schema.oaf.Result;
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public class SparkAtomicActionScoreJobTest {
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@ -73,15 +73,16 @@ public class SparkAtomicActionScoreJobTest {
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}
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private void runJob(String inputPath, String outputPath, String targetEntity) throws Exception {
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SparkAtomicActionScoreJob.main(
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SparkAtomicActionScoreJob
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.main(
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new String[] {
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"-isSparkSessionManaged", Boolean.FALSE.toString(),
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"-inputPath", inputPath,
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"-outputPath", outputPath,
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"-targetEntity", targetEntity,
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});
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}
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);
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}
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@Test
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void testResultScores() throws Exception {
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final String targetEntity = RESULT;
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@ -171,7 +172,8 @@ public class SparkAtomicActionScoreJobTest {
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// count that the project with id testProjectId is present
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assertEquals(1, projects.filter(row -> row.getId().equals(testProjectId)).count());
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projects.filter(row -> row.getId().equals(testProjectId))
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projects
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.filter(row -> row.getId().equals(testProjectId))
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.flatMap(r -> r.getMeasures().iterator())
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.foreach(m -> {
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log.info(m.getId() + " " + m.getUnit());
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@ -184,7 +186,7 @@ public class SparkAtomicActionScoreJobTest {
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// ensure that the correct key is provided, i.e. score
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assertEquals("score", kv.getKey());
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switch(m.getId()) {
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switch (m.getId()) {
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case "numOfInfluentialResults":
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assertEquals("0", kv.getValue());
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break;
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@ -92,7 +92,7 @@ public class PrepareH2020ProgrammeTest {
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Assertions.assertEquals(0, verificationDataset.filter("classification = ''").count());
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//tmp.foreach(csvProgramme -> System.out.println(OBJECT_MAPPER.writeValueAsString(csvProgramme)));
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// tmp.foreach(csvProgramme -> System.out.println(OBJECT_MAPPER.writeValueAsString(csvProgramme)));
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Assertions
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.assertEquals(
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@ -98,7 +98,7 @@ public class ReadProjectsTest {
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Assertions.assertEquals("H2020-EU.1.3.", project.getLegalBasis());
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Assertions.assertEquals("MSCA-IF-2019", project.getTopics());
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//tmp.foreach(p -> System.out.println(OBJECT_MAPPER.writeValueAsString(p)));
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// tmp.foreach(p -> System.out.println(OBJECT_MAPPER.writeValueAsString(p)));
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}
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}
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@ -93,7 +93,7 @@ public class ReadTopicTest {
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Assertions.assertEquals("Individual Fellowships", topic.getTitle());
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Assertions.assertEquals("MSCA-IF-2019", topic.getTopic());
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//tmp.foreach(p -> System.out.println(OBJECT_MAPPER.writeValueAsString(p)));
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// tmp.foreach(p -> System.out.println(OBJECT_MAPPER.writeValueAsString(p)));
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}
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}
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@ -97,7 +97,7 @@ oozie.wf.application.path=${oozieTopWfApplicationPath}
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# Path where the final output should be?
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actionSetOutputPath=${workingDir}/bip_actionsets/
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actionSetOutputPath=${workingDir}/bip_actionsets
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# The directory to store project impact indicators
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projectImpactIndicatorsOutput=${workingDir}/project_indicators
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@ -24,20 +24,21 @@
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<case to="spark-impulse">${wf:conf('resume') eq "impulse"}</case>
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<case to="spark-pagerank">${wf:conf('resume') eq "pagerank"}</case>
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<case to="spark-attrank">${wf:conf('resume') eq "attrank"}</case>
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<!-- Removed for serafeim -->
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<!-- <case to="iterative-rankings">${wf:conf('resume') eq "rankings-iterative"}</case> -->
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<case to="get-file-names">${wf:conf('resume') eq "format-results"}</case>
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<case to="map-openaire-to-doi">${wf:conf('resume') eq "map-ids"}</case>
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<case to="map-scores-to-dois">${wf:conf('resume') eq "map-scores"}</case>
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<case to="create-openaire-ranking-graph">${wf:conf('resume') eq "start"}</case>
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<case to="project-impact-indicators">${wf:conf('resume') eq "projects-impact"}</case>
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<!-- TODO: add action set creation here -->
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<!-- Aggregation of impact scores on the project level -->
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<case to="project-impact-indicators">${wf:conf('resume') eq "projects-impact"}</case>
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<case to="create-actionset-for-projects">${wf:conf('resume') eq "projects-impact-actionsets"}</case>
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<default to="create-openaire-ranking-graph" />
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</switch>
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</decision>
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<!-- Script here written by Serafeim: maps openaire ids to their synonyms -->
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<!-- maps openaire ids to their synonyms -->
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<action name="create-openaire-ranking-graph">
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<!-- This is required as a tag for spark jobs, regardless of programming language -->
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<spark xmlns="uri:oozie:spark-action:0.2">
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@ -479,7 +480,7 @@
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<!-- Finish formatting data and end -->
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<join name="join-file-formatting" to="map-openaire-to-doi"/>
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<!-- Script here written by Serafeim: maps openaire ids to their synonyms -->
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<!-- maps openaire ids to their synonyms -->
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<action name="map-openaire-to-doi">
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<!-- This is required as a tag for spark jobs, regardless of programming language -->
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<spark xmlns="uri:oozie:spark-action:0.2">
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@ -526,7 +527,7 @@
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</action>
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<!-- Script here written by Serafeim: maps openaire ids to their synonyms -->
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<!-- maps openaire ids to their synonyms -->
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<action name="map-scores-to-dois">
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<!-- This is required as a tag for spark jobs, regardless of programming language -->
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<spark xmlns="uri:oozie:spark-action:0.2">
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@ -568,14 +569,14 @@
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</spark>
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<!-- Do this after finishing okay -->
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<ok to="deleteOutputPathForActionSet" />
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<!-- This is the initial code <ok to="deleteOutputPathForActionSet" /> -->
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<ok to="delete-output-path-for-actionset" />
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<!-- This is the initial code <ok to="delete-output-path-for-actionset" /> -->
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<!-- Go there if we have an error -->
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<error to="map-scores-fail" />
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</action>
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<action name="deleteOutputPathForActionSet">
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<action name="delete-output-path-for-actionset">
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<fs>
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<delete path="${actionSetOutputPath}/results/"/>
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<delete path="${actionSetOutputPath}/projects/"/>
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@ -583,13 +584,13 @@
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<mkdir path="${actionSetOutputPath}/results/"/>
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<mkdir path="${actionSetOutputPath}/projects/"/>
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</fs>
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<ok to="createActionSetForResults"/>
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<ok to="create-actionset-for-results"/>
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<error to="actionset-delete-fail"/>
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</action>
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<action name="createActionSetForResults">
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<action name="create-actionset-for-results">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Produces the atomic action with the bip finder scores for publications</name>
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<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
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@ -640,7 +641,7 @@
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<!-- Script arguments here -->
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<!-- graph data folder from which to read relations -->
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<arg>${openaireDataInput}/relations</arg>
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<arg>${openaireDataInput}/relation</arg>
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<!-- input files with impact indicators for results -->
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<arg>${nameNode}/${workingDir}/${wf:actionData('get-file-names')['pr_file']}</arg>
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@ -658,16 +659,16 @@
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</spark>
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<!-- Do this after finishing okay -->
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<ok to="createActionSetForProjects" />
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<ok to="create-actionset-for-projects" />
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<!-- Go there if we have an error -->
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<error to="project-impact-indicators-fail" />
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</action>
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<action name="createActionSetForProjects">
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<action name="create-actionset-for-projects">
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<spark xmlns="uri:oozie:spark-action:0.2">
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<master>yarn</master>
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<master>yarn-cluster</master>
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<mode>cluster</mode>
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<name>Produces the atomic action with the bip finder scores for projects</name>
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<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
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