forked from D-Net/dnet-hadoop
Merge branch '8172_impact_indicators_workflow' of https://code-repo.d4science.org/D-Net/dnet-hadoop into 8172_impact_indicators_workflow
This commit is contained in:
commit
06b9b71c4e
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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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@ -98,17 +97,18 @@ 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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return project;
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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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new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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.saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
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.toJavaRDD()
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.map(p -> new AtomicAction(Project.class, 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(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);
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}
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@ -1,69 +1,74 @@
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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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@Getter
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@Setter
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public class BipProjectModel {
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String projectId;
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String projectId;
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String numOfInfluentialResults;
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String numOfInfluentialResults;
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String numOfPopularResults;
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String numOfPopularResults;
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String totalImpulse;
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String totalImpulse;
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String totalCitationCount;
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String totalCitationCount;
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// each project bip measure has exactly one value, hence one key-value pair
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private Measure createMeasure(String measureId, String measureValue) {
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// each project bip measure has exactly one value, hence one key-value pair
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private Measure createMeasure(String measureId, String measureValue) {
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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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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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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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KeyValue kv = new KeyValue();
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kv.setKey("score");
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kv.setValue(measureValue);
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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
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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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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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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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}
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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
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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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||||
|
||||
}
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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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||||
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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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||||
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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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|
|
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|
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@ -24,8 +24,8 @@ import org.slf4j.LoggerFactory;
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|||
|
||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||
|
||||
import eu.dnetlib.dhp.actionmanager.bipmodel.score.deserializers.BipResultModel;
|
||||
import eu.dnetlib.dhp.actionmanager.bipmodel.BipScore;
|
||||
import eu.dnetlib.dhp.actionmanager.bipmodel.score.deserializers.BipResultModel;
|
||||
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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||||
|
|
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|
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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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|
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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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||||
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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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||||
new String[] {
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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,
|
||||
"-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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@ -149,8 +150,8 @@ public class SparkAtomicActionScoreJobTest {
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void testProjectScores() throws Exception {
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String targetEntity = PROJECT;
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String inputResultScores = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/project_bip_scores.json")
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.getPath();
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.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/project_bip_scores.json")
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.getPath();
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String outputPath = workingDir.toString() + "/" + targetEntity + "/actionSet";
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// execute the job to generate the action sets for project scores
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@ -159,9 +160,9 @@ public class SparkAtomicActionScoreJobTest {
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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|
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JavaRDD<Project> projects = sc
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.sequenceFile(outputPath, Text.class, Text.class)
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
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.map(aa -> ((Project) aa.getPayload()));
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.sequenceFile(outputPath, Text.class, Text.class)
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.map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class))
|
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.map(aa -> ((Project) aa.getPayload()));
|
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|
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// test the number of projects
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assertEquals(4, projects.count());
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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());
|
||||
|
||||
projects.filter(row -> row.getId().equals(testProjectId))
|
||||
projects
|
||||
.filter(row -> row.getId().equals(testProjectId))
|
||||
.flatMap(r -> r.getMeasures().iterator())
|
||||
.foreach(m -> {
|
||||
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
|
||||
assertEquals("score", kv.getKey());
|
||||
|
||||
switch(m.getId()) {
|
||||
switch (m.getId()) {
|
||||
case "numOfInfluentialResults":
|
||||
assertEquals("0", kv.getValue());
|
||||
break;
|
||||
|
|
|
|||
|
|
@ -92,7 +92,7 @@ public class PrepareH2020ProgrammeTest {
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|||
|
||||
Assertions.assertEquals(0, verificationDataset.filter("classification = ''").count());
|
||||
|
||||
//tmp.foreach(csvProgramme -> System.out.println(OBJECT_MAPPER.writeValueAsString(csvProgramme)));
|
||||
// tmp.foreach(csvProgramme -> System.out.println(OBJECT_MAPPER.writeValueAsString(csvProgramme)));
|
||||
|
||||
Assertions
|
||||
.assertEquals(
|
||||
|
|
|
|||
|
|
@ -98,7 +98,7 @@ public class ReadProjectsTest {
|
|||
Assertions.assertEquals("H2020-EU.1.3.", project.getLegalBasis());
|
||||
Assertions.assertEquals("MSCA-IF-2019", project.getTopics());
|
||||
|
||||
//tmp.foreach(p -> System.out.println(OBJECT_MAPPER.writeValueAsString(p)));
|
||||
// tmp.foreach(p -> System.out.println(OBJECT_MAPPER.writeValueAsString(p)));
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -93,7 +93,7 @@ public class ReadTopicTest {
|
|||
Assertions.assertEquals("Individual Fellowships", topic.getTitle());
|
||||
Assertions.assertEquals("MSCA-IF-2019", topic.getTopic());
|
||||
|
||||
//tmp.foreach(p -> System.out.println(OBJECT_MAPPER.writeValueAsString(p)));
|
||||
// tmp.foreach(p -> System.out.println(OBJECT_MAPPER.writeValueAsString(p)));
|
||||
|
||||
}
|
||||
}
|
||||
|
|
|
|||
|
|
@ -97,7 +97,7 @@ oozie.wf.application.path=${oozieTopWfApplicationPath}
|
|||
|
||||
|
||||
# Path where the final output should be?
|
||||
actionSetOutputPath=${workingDir}/bip_actionsets/
|
||||
actionSetOutputPath=${workingDir}/bip_actionsets
|
||||
|
||||
# The directory to store project impact indicators
|
||||
projectImpactIndicatorsOutput=${workingDir}/project_indicators
|
||||
|
|
|
|||
|
|
@ -13,7 +13,6 @@
|
|||
</global>
|
||||
|
||||
<!-- start using a decision node, so as to determine from which point onwards a job will continue -->
|
||||
<!-- <start to="get-doi-synonyms" /> -->
|
||||
<start to="entry-point-decision" />
|
||||
|
||||
<decision name="entry-point-decision">
|
||||
|
|
@ -24,40 +23,28 @@
|
|||
<case to="spark-impulse">${wf:conf('resume') eq "impulse"}</case>
|
||||
<case to="spark-pagerank">${wf:conf('resume') eq "pagerank"}</case>
|
||||
<case to="spark-attrank">${wf:conf('resume') eq "attrank"}</case>
|
||||
<!-- Removed for serafeim -->
|
||||
<!-- <case to="iterative-rankings">${wf:conf('resume') eq "rankings-iterative"}</case> -->
|
||||
<case to="get-file-names">${wf:conf('resume') eq "format-results"}</case>
|
||||
<case to="map-openaire-to-doi">${wf:conf('resume') eq "map-ids"}</case>
|
||||
<case to="map-scores-to-dois">${wf:conf('resume') eq "map-scores"}</case>
|
||||
<case to="create-openaire-ranking-graph">${wf:conf('resume') eq "start"}</case>
|
||||
<case to="project-impact-indicators">${wf:conf('resume') eq "projects-impact"}</case>
|
||||
|
||||
<!-- TODO: add action set creation here -->
|
||||
<!-- Aggregation of impact scores on the project level -->
|
||||
<case to="project-impact-indicators">${wf:conf('resume') eq "projects-impact"}</case>
|
||||
<case to="create-actionset-for-projects">${wf:conf('resume') eq "projects-impact-actionsets"}</case>
|
||||
|
||||
<default to="create-openaire-ranking-graph" />
|
||||
</switch>
|
||||
</decision>
|
||||
|
||||
<!-- Script here written by Serafeim: maps openaire ids to their synonyms -->
|
||||
<!-- initial step: create citation network -->
|
||||
<action name="create-openaire-ranking-graph">
|
||||
<!-- This is required as a tag for spark jobs, regardless of programming language -->
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
|
||||
<!-- Delete previously created doi synonym folder -->
|
||||
<!-- I think we don't need this given we don't have synonyms anymore
|
||||
<prepare>
|
||||
<delete path="${synonymFolder}"/>
|
||||
</prepare>
|
||||
-->
|
||||
|
||||
<!-- using configs from an example on openaire -->
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
|
||||
<!-- This is the name of our job -->
|
||||
<name>Openaire Ranking Graph Creation</name>
|
||||
<!-- Script name goes here -->
|
||||
<name>OpenAIRE Ranking Graph Creation</name>
|
||||
<jar>create_openaire_ranking_graph.py</jar>
|
||||
<!-- spark configuration options: I've taken most of them from an example from dhp workflows / Master value stolen from sandro -->
|
||||
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkHighExecutorMemory}
|
||||
|
|
@ -79,39 +66,30 @@
|
|||
<arg>${sparkShufflePartitions}</arg>
|
||||
<!-- The output of the graph should be the openaire input graph for ranking-->
|
||||
<arg>${openaireGraphInputPath}</arg>
|
||||
<!-- This needs to point to the file on the hdfs i think -->
|
||||
|
||||
<file>${wfAppPath}/create_openaire_ranking_graph.py#create_openaire_ranking_graph.py</file>
|
||||
</spark>
|
||||
|
||||
<!-- Do this after finishing okay -->
|
||||
<ok to="non-iterative-rankings" />
|
||||
<!-- Go there if we have an error -->
|
||||
<error to="openaire-graph-error" />
|
||||
|
||||
</action>
|
||||
|
||||
<!-- Citation Count and RAM are calculated in parallel-->
|
||||
<!-- Impulse Requires resources and will be run after-->
|
||||
<fork name="non-iterative-rankings">
|
||||
<path start="spark-cc"/>
|
||||
<!-- <path start="spark-impulse"/> -->
|
||||
<path start="spark-ram"/>
|
||||
</fork>
|
||||
|
||||
<!-- CC here -->
|
||||
<!-- Run Citation Count calculation -->
|
||||
<action name="spark-cc">
|
||||
<!-- This is required as a tag for spark jobs, regardless of programming language -->
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
|
||||
<!-- using configs from an example on openaire -->
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
|
||||
<!-- This is the name of our job -->
|
||||
<name>Spark CC</name>
|
||||
<!-- Script name goes here -->
|
||||
<name>Citation Count calculation</name>
|
||||
<jar>CC.py</jar>
|
||||
<!-- spark configuration options: I've taken most of them from an example from dhp workflows / Master value stolen from sandro -->
|
||||
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkHighExecutorMemory}
|
||||
|
|
@ -128,31 +106,23 @@
|
|||
<arg>${openaireGraphInputPath}</arg>
|
||||
<!-- number of partitions to be used on joins -->
|
||||
<arg>${sparkShufflePartitions}</arg>
|
||||
<!-- This needs to point to the file on the hdfs i think -->
|
||||
|
||||
<file>${wfAppPath}/bip-ranker/CC.py#CC.py</file>
|
||||
</spark>
|
||||
|
||||
<!-- Do this after finishing okay -->
|
||||
<ok to="join-non-iterative-rankings" />
|
||||
<!-- Go there if we have an error -->
|
||||
<error to="cc-fail" />
|
||||
|
||||
</action>
|
||||
|
||||
<!-- IMPULSE here -->
|
||||
<!-- RAM calculation -->
|
||||
<action name="spark-ram">
|
||||
<!-- This is required as a tag for spark jobs, regardless of programming language -->
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
|
||||
<!-- using configs from an example on openaire -->
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
|
||||
<!-- This is the name of our job -->
|
||||
<name>Spark RAM</name>
|
||||
<!-- Script name goes here -->
|
||||
<name>RAM calculation</name>
|
||||
<jar>TAR.py</jar>
|
||||
<!-- spark configuration options: I've taken most of them from an example from dhp workflows / Master value stolen from sandro -->
|
||||
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkHighExecutorMemory}
|
||||
|
|
@ -170,37 +140,27 @@
|
|||
<arg>${ramGamma}</arg>
|
||||
<arg>${currentYear}</arg>
|
||||
<arg>RAM</arg>
|
||||
<!-- number of partitions to be used on joins -->
|
||||
<arg>${sparkShufflePartitions}</arg>
|
||||
<arg>${checkpointDir}</arg>
|
||||
<!-- This needs to point to the file on the hdfs i think -->
|
||||
|
||||
<file>${wfAppPath}/bip-ranker/TAR.py#TAR.py</file>
|
||||
</spark>
|
||||
|
||||
<!-- Do this after finishing okay -->
|
||||
<ok to="join-non-iterative-rankings" />
|
||||
<!-- Go there if we have an error -->
|
||||
<error to="ram-fail" />
|
||||
|
||||
</action>
|
||||
|
||||
<!-- JOIN NON-ITERATIVE METHODS AND THEN CONTINUE TO ITERATIVE ONES -->
|
||||
<!-- Join non-iterative methods -->
|
||||
<join name="join-non-iterative-rankings" to="spark-impulse"/>
|
||||
|
||||
<!-- IMPULSE here -->
|
||||
<action name="spark-impulse">
|
||||
<!-- This is required as a tag for spark jobs, regardless of programming language -->
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
|
||||
<!-- using configs from an example on openaire -->
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
|
||||
<!-- This is the name of our job -->
|
||||
<name>Spark Impulse</name>
|
||||
<!-- Script name goes here -->
|
||||
<name>Impulse calculation</name>
|
||||
<jar>CC.py</jar>
|
||||
<!-- spark configuration options: I've taken most of them from an example from dhp workflows / Master value stolen from sandro -->
|
||||
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkHighExecutorMemory}
|
||||
|
|
@ -218,47 +178,22 @@
|
|||
<!-- number of partitions to be used on joins -->
|
||||
<arg>${sparkShufflePartitions}</arg>
|
||||
<arg>3</arg>
|
||||
<!-- This needs to point to the file on the hdfs i think -->
|
||||
|
||||
<file>${wfAppPath}/bip-ranker/CC.py#CC.py</file>
|
||||
</spark>
|
||||
|
||||
<!-- Do this after finishing okay -->
|
||||
<ok to="spark-pagerank" />
|
||||
<!-- Go there if we have an error -->
|
||||
<error to="impulse-fail" />
|
||||
|
||||
</action>
|
||||
|
||||
<!-- Removed for ser to make pagerank & attrank serial -->
|
||||
<!--
|
||||
<fork name="iterative-rankings">
|
||||
<path start="spark-pagerank"/>
|
||||
<path start="spark-attrank"/>
|
||||
</fork>
|
||||
-->
|
||||
|
||||
<!-- PAGERANK here -->
|
||||
<action name="spark-pagerank">
|
||||
<!-- This is required as a tag for spark jobs, regardless of programming language -->
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
|
||||
<!-- we could add map-reduce configs here, but I don't know if we need them -->
|
||||
<!-- This is the type of master-client configuration for running spark -->
|
||||
<!-- <master>yarn-client</master> -->
|
||||
<!-- Reference says: The master element indicates the url of the Spark Master. Ex: spark://host:port, mesos://host:port, yarn-cluster, yarn-master, or local. -->
|
||||
<!-- <master>local[*]</master> -->
|
||||
<!-- Reference says: The mode element if present indicates the mode of spark, where to run spark driver program. Ex: client,cluster. | In my case I always have a client -->
|
||||
<!-- <mode>client</mode> -->
|
||||
|
||||
<!-- using configs from an example on openaire -->
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
|
||||
<!-- This is the name of our job -->
|
||||
<name>Spark Pagerank</name>
|
||||
<!-- Script name goes here -->
|
||||
<name>Pagerank calculation</name>
|
||||
<jar>PageRank.py</jar>
|
||||
<!-- spark configuration options: I've taken most of them from an example from dhp workflows / Master value stolen from sandro -->
|
||||
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkHighExecutorMemory}
|
||||
|
|
@ -279,31 +214,22 @@
|
|||
<!-- number of partitions to be used on joins -->
|
||||
<arg>${sparkShufflePartitions}</arg>
|
||||
<arg>dfs</arg>
|
||||
<!-- This needs to point to the file on the hdfs i think -->
|
||||
|
||||
<file>${wfAppPath}/bip-ranker/PageRank.py#PageRank.py</file>
|
||||
</spark>
|
||||
|
||||
<!-- Do this after finishing okay -->
|
||||
<ok to="spark-attrank" />
|
||||
<!-- Go there if we have an error -->
|
||||
<error to="pagerank-fail" />
|
||||
|
||||
</action>
|
||||
|
||||
<!-- ATTRANK here -->
|
||||
<action name="spark-attrank">
|
||||
<!-- This is required as a tag for spark jobs, regardless of programming language -->
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
|
||||
<!-- using configs from an example on openaire -->
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
|
||||
<!-- This is the name of our job -->
|
||||
<name>Spark AttRank</name>
|
||||
<!-- Script name goes here -->
|
||||
<name>AttRank calculation</name>
|
||||
<jar>AttRank.py</jar>
|
||||
<!-- spark configuration options: I've taken most of them from an example from dhp workflows / Master value stolen from sandro -->
|
||||
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkHighExecutorMemory}
|
||||
|
|
@ -329,27 +255,16 @@
|
|||
<!-- number of partitions to be used on joins -->
|
||||
<arg>${sparkShufflePartitions}</arg>
|
||||
<arg>dfs</arg>
|
||||
<!-- This needs to point to the file on the hdfs i think -->
|
||||
|
||||
<file>${wfAppPath}/bip-ranker/AttRank.py#AttRank.py</file>
|
||||
</spark>
|
||||
|
||||
<!-- Do this after finishing okay -->
|
||||
<ok to="get-file-names" />
|
||||
<!-- Go there if we have an error -->
|
||||
<error to="attrank-fail" />
|
||||
|
||||
</action>
|
||||
|
||||
<!-- Removed for ser -->
|
||||
<!--
|
||||
JOIN ITERATIVE METHODS AND THEN END =
|
||||
<join name="join-iterative-rankings" to="end" />
|
||||
to="get-file-names"/>
|
||||
-->
|
||||
|
||||
<!-- This will be a shell action that will output key-value pairs for output files -->
|
||||
<action name="get-file-names">
|
||||
<!-- This is required as a tag for shell jobs -->
|
||||
<shell xmlns="uri:oozie:shell-action:0.3">
|
||||
|
||||
<!-- Exec is needed for shell commands - points to type of shell command -->
|
||||
|
|
@ -359,15 +274,12 @@
|
|||
<!-- We only pass the directory where we expect to find the rankings -->
|
||||
<argument>${workingDir}</argument>
|
||||
|
||||
<!-- the name of the file run -->
|
||||
<file>${wfAppPath}/get_ranking_files.sh#get_ranking_files.sh</file>
|
||||
<!-- Get the output in order to be usable by following actions -->
|
||||
<capture-output/>
|
||||
</shell>
|
||||
|
||||
<!-- Do this after finishing okay -->
|
||||
<ok to="format-result-files" />
|
||||
<!-- Go there if we have an error -->
|
||||
<error to="filename-getting-error" />
|
||||
|
||||
</action>
|
||||
|
|
@ -382,18 +294,12 @@
|
|||
<!-- Format json files -->
|
||||
<!-- Two parts: a) format files b) make the file endings .json.gz -->
|
||||
<action name="format-json-files">
|
||||
<!-- This is required as a tag for spark jobs, regardless of programming language -->
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
|
||||
<!-- using configs from an example on openaire -->
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
|
||||
<!-- This is the name of our job -->
|
||||
<name>Format Ranking Results JSON</name>
|
||||
<!-- Script name goes here -->
|
||||
<jar>format_ranking_results.py</jar>
|
||||
<!-- spark configuration options: I've taken most of them from an example from dhp workflows / Master value stolen from sandro -->
|
||||
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkNormalExecutorMemory}
|
||||
|
|
@ -418,13 +324,11 @@
|
|||
<arg>${sparkShufflePartitions}</arg>
|
||||
<!-- Type of data to be produced [bip (dois) / openaire (openaire-ids) ] -->
|
||||
<arg>openaire</arg>
|
||||
<!-- This needs to point to the file on the hdfs i think -->
|
||||
|
||||
<file>${wfAppPath}/format_ranking_results.py#format_ranking_results.py</file>
|
||||
</spark>
|
||||
|
||||
<!-- Do this after finishing okay -->
|
||||
<ok to="join-file-formatting" />
|
||||
<!-- Go there if we have an error -->
|
||||
<error to="json-formatting-fail" />
|
||||
</action>
|
||||
|
||||
|
|
@ -470,18 +374,15 @@
|
|||
<file>${wfAppPath}/format_ranking_results.py#format_ranking_results.py</file>
|
||||
</spark>
|
||||
|
||||
<!-- Do this after finishing okay -->
|
||||
<ok to="join-file-formatting" />
|
||||
<!-- Go there if we have an error -->
|
||||
<error to="bip-formatting-fail" />
|
||||
</action>
|
||||
|
||||
<!-- Finish formatting data and end -->
|
||||
<!-- Finish formatting jobs -->
|
||||
<join name="join-file-formatting" to="map-openaire-to-doi"/>
|
||||
|
||||
<!-- Script here written by Serafeim: maps openaire ids to their synonyms -->
|
||||
<!-- maps openaire ids to DOIs -->
|
||||
<action name="map-openaire-to-doi">
|
||||
<!-- This is required as a tag for spark jobs, regardless of programming language -->
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
|
||||
<!-- Delete previously created doi synonym folder -->
|
||||
|
|
@ -489,15 +390,10 @@
|
|||
<delete path="${synonymFolder}"/>
|
||||
</prepare>
|
||||
|
||||
<!-- using configs from an example on openaire -->
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
|
||||
<!-- This is the name of our job -->
|
||||
<name>Openaire-DOI synonym collection</name>
|
||||
<!-- Script name goes here -->
|
||||
<jar>map_openaire_ids_to_dois.py</jar>
|
||||
<!-- spark configuration options: I've taken most of them from an example from dhp workflows / Master value stolen from sandro -->
|
||||
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkHighExecutorMemory}
|
||||
|
|
@ -514,19 +410,16 @@
|
|||
<arg>${openaireDataInput}/</arg>
|
||||
<!-- number of partitions to be used on joins -->
|
||||
<arg>${synonymFolder}</arg>
|
||||
<!-- This needs to point to the file on the hdfs i think -->
|
||||
|
||||
<file>${wfAppPath}/map_openaire_ids_to_dois.py#map_openaire_ids_to_dois.py</file>
|
||||
</spark>
|
||||
|
||||
<!-- Do this after finishing okay -->
|
||||
<ok to="map-scores-to-dois" />
|
||||
<!-- Go there if we have an error -->
|
||||
<error to="synonym-collection-fail" />
|
||||
|
||||
</action>
|
||||
|
||||
|
||||
<!-- Script here written by Serafeim: maps openaire ids to their synonyms -->
|
||||
<!-- mapping openaire scores to DOIs -->
|
||||
<action name="map-scores-to-dois">
|
||||
<!-- This is required as a tag for spark jobs, regardless of programming language -->
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
|
|
@ -534,12 +427,8 @@
|
|||
<!-- using configs from an example on openaire -->
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
|
||||
<!-- This is the name of our job -->
|
||||
<name>Mapping Openaire Scores to DOIs</name>
|
||||
<!-- Script name goes here -->
|
||||
<jar>map_scores_to_dois.py</jar>
|
||||
<!-- spark configuration options: I've taken most of them from an example from dhp workflows / Master value stolen from sandro -->
|
||||
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkHighExecutorMemory}
|
||||
|
|
@ -563,19 +452,16 @@
|
|||
<arg>${nameNode}/${workingDir}/${wf:actionData('get-file-names')['impulse_file']}</arg>
|
||||
<arg>${nameNode}/${workingDir}/${wf:actionData('get-file-names')['ram_file']}</arg>
|
||||
|
||||
<!-- This needs to point to the file on the hdfs i think -->
|
||||
<file>${wfAppPath}/map_scores_to_dois.py#map_scores_to_dois.py</file>
|
||||
</spark>
|
||||
|
||||
<!-- Do this after finishing okay -->
|
||||
<ok to="deleteOutputPathForActionSet" />
|
||||
<!-- This is the initial code <ok to="deleteOutputPathForActionSet" /> -->
|
||||
<!-- Go there if we have an error -->
|
||||
<ok to="delete-output-path-for-actionset" />
|
||||
<error to="map-scores-fail" />
|
||||
|
||||
</action>
|
||||
|
||||
<action name="deleteOutputPathForActionSet">
|
||||
<!-- Re-create folder for result and project actionsets -->
|
||||
<action name="delete-output-path-for-actionset">
|
||||
<fs>
|
||||
<delete path="${actionSetOutputPath}/results/"/>
|
||||
<delete path="${actionSetOutputPath}/projects/"/>
|
||||
|
|
@ -583,17 +469,19 @@
|
|||
<mkdir path="${actionSetOutputPath}/results/"/>
|
||||
<mkdir path="${actionSetOutputPath}/projects/"/>
|
||||
</fs>
|
||||
<ok to="createActionSetForResults"/>
|
||||
<ok to="create-actionset-for-results"/>
|
||||
<error to="actionset-delete-fail"/>
|
||||
</action>
|
||||
|
||||
<action name="createActionSetForResults">
|
||||
<action name="create-actionset-for-results">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Produces the atomic action with the bip finder scores for publications</name>
|
||||
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkNormalExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
|
|
@ -608,23 +496,19 @@
|
|||
<arg>--outputPath</arg><arg>${actionSetOutputPath}/results/</arg>
|
||||
<arg>--targetEntity</arg><arg>result</arg>
|
||||
</spark>
|
||||
|
||||
<ok to="project-impact-indicators"/>
|
||||
<error to="actionset-creation-fail"/>
|
||||
|
||||
</action>
|
||||
|
||||
<action name="project-impact-indicators">
|
||||
<!-- This is required as a tag for spark jobs, regardless of programming language -->
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
|
||||
<!-- using configs from an example on openaire -->
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
|
||||
<!-- This is the name of our job -->
|
||||
<name>Project Impact Indicators</name>
|
||||
<!-- Script name goes here -->
|
||||
<name>Project Impact Indicators calculation</name>
|
||||
<jar>projects_impact.py</jar>
|
||||
<!-- spark configuration options: I've taken most of them from an example from dhp workflows / Master value stolen from sandro -->
|
||||
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkHighExecutorMemory}
|
||||
|
|
@ -638,9 +522,8 @@
|
|||
</spark-opts>
|
||||
|
||||
<!-- Script arguments here -->
|
||||
|
||||
<!-- graph data folder from which to read relations -->
|
||||
<arg>${openaireDataInput}/relations</arg>
|
||||
<arg>${openaireDataInput}/relation</arg>
|
||||
|
||||
<!-- input files with impact indicators for results -->
|
||||
<arg>${nameNode}/${workingDir}/${wf:actionData('get-file-names')['pr_file']}</arg>
|
||||
|
|
@ -652,26 +535,23 @@
|
|||
<arg>${sparkShufflePartitions}</arg>
|
||||
|
||||
<arg>${projectImpactIndicatorsOutput}</arg>
|
||||
|
||||
<!-- This needs to point to the file on the hdfs i think -->
|
||||
<file>${wfAppPath}/projects_impact.py#projects_impact.py</file>
|
||||
</spark>
|
||||
|
||||
<!-- Do this after finishing okay -->
|
||||
<ok to="createActionSetForProjects" />
|
||||
|
||||
<!-- Go there if we have an error -->
|
||||
<ok to="create-actionset-for-projects" />
|
||||
<error to="project-impact-indicators-fail" />
|
||||
|
||||
</action>
|
||||
|
||||
<action name="createActionSetForProjects">
|
||||
<action name="create-actionset-for-projects">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
<master>yarn</master>
|
||||
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Produces the atomic action with the bip finder scores for projects</name>
|
||||
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
|
||||
<spark-opts>
|
||||
--executor-memory=${sparkNormalExecutorMemory}
|
||||
--executor-cores=${sparkExecutorCores}
|
||||
|
|
@ -682,12 +562,15 @@
|
|||
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
|
||||
<arg>--inputPath</arg><arg>${projectImpactIndicatorsOutput}</arg>
|
||||
<arg>--outputPath</arg><arg>${actionSetOutputPath}/projects/</arg>
|
||||
<arg>--targetEntity</arg><arg>project</arg>
|
||||
</spark>
|
||||
|
||||
<ok to="end"/>
|
||||
<error to="actionset-project-creation-fail"/>
|
||||
|
||||
</action>
|
||||
|
||||
<!-- Definitions of failure messages -->
|
||||
|
|
|
|||
Loading…
Reference in New Issue