Add actionsets for project impact indicators
This commit is contained in:
Serafeim Chatzopoulos
parent
23f58a86f1
commit
ee04cf92bf
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@ -9,6 +9,7 @@ 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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@ -24,7 +25,7 @@ import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.bipmodel.BipDeserialize;
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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.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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@ -56,18 +57,17 @@ public class SparkAtomicActionScoreJob implements Serializable {
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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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Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("inputPath");
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log.info("inputPath {}: ", inputPath);
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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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log.info("outputPath: {}", outputPath);
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final String targetEntity = parser.get("targetEntity");
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log.info("targetEntity: {}", targetEntity);
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SparkConf conf = new SparkConf();
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@ -76,17 +76,48 @@ public class SparkAtomicActionScoreJob implements Serializable {
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isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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prepareResults(spark, inputPath, outputPath);
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});
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// follow different procedures for different target entities
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switch (targetEntity) {
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case "result":
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prepareResults(spark, inputPath, outputPath);
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break;
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case "project":
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prepareProjects(spark, inputPath, outputPath);
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break;
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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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private static <I extends Project> void prepareProjects(SparkSession spark, String inputPath, String outputPath) {
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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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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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}
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private static <I extends Result> void prepareResults(SparkSession spark, String bipScorePath, String outputPath) {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc
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JavaRDD<BipResultModel> bipDeserializeJavaRDD = sc
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.textFile(bipScorePath)
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.map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class));
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.map(item -> OBJECT_MAPPER.readValue(item, BipResultModel.class));
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Dataset<BipScore> bipScores = spark
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.createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> {
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@ -159,12 +190,4 @@ public class SparkAtomicActionScoreJob implements Serializable {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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public static <R> Dataset<R> readPath(
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SparkSession spark, String inputPath, Class<R> clazz) {
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return spark
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.read()
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.textFile(inputPath)
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.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz));
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}
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}
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@ -0,0 +1,69 @@
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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 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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@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 numOfInfluentialResults;
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String numOfPopularResults;
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String totalImpulse;
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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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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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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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}
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@ -1,5 +1,7 @@
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package eu.dnetlib.dhp.actionmanager.bipmodel;
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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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@ -11,9 +13,9 @@ import java.util.List;
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* Only needed for deserialization purposes
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*/
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public class BipDeserialize extends HashMap<String, List<Score>> implements Serializable {
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public class BipResultModel extends HashMap<String, List<Score>> implements Serializable {
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public BipDeserialize() {
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public BipResultModel() {
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super();
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}
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@ -24,7 +24,7 @@ import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.bipmodel.BipDeserialize;
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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.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.common.HdfsSupport;
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@ -82,9 +82,9 @@ public class PrepareBipFinder implements Serializable {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaRDD<BipDeserialize> bipDeserializeJavaRDD = sc
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JavaRDD<BipResultModel> bipDeserializeJavaRDD = sc
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.textFile(inputPath)
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.map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class));
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.map(item -> OBJECT_MAPPER.readValue(item, BipResultModel.class));
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spark
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.createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> {
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@ -16,5 +16,11 @@
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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": "te",
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"paramLongName": "targetEntity",
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"paramDescription": "the type of target entity to be enriched; currently supported one of { 'result', 'project' }",
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"paramRequired": true
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}
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]
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@ -6,8 +6,9 @@ import static org.junit.jupiter.api.Assertions.*;
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import java.io.IOException;
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import java.nio.file.Files;
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import java.nio.file.Path;
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import java.util.List;
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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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@ -27,7 +28,6 @@ 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.Publication;
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import eu.dnetlib.dhp.schema.oaf.Result;
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public class SparkAtomicActionScoreJobTest {
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@ -37,8 +37,11 @@ public class SparkAtomicActionScoreJobTest {
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private static SparkSession spark;
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private static Path workingDir;
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private static final Logger log = LoggerFactory
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.getLogger(SparkAtomicActionScoreJobTest.class);
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private final static String RESULT = "result";
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private final static String PROJECT = "project";
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private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionScoreJobTest.class);
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@BeforeAll
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public static void beforeAll() throws IOException {
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@ -69,29 +72,31 @@ public class SparkAtomicActionScoreJobTest {
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spark.stop();
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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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"-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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@Test
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void testMatch() throws Exception {
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String bipScoresPath = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/bip_scores_oid.json")
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void testResultScores() throws Exception {
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final String targetEntity = RESULT;
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String inputResultScores = getClass()
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.getResource("/eu/dnetlib/dhp/actionmanager/bipfinder/result_bip_scores.json")
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.getPath();
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String outputPath = workingDir.toString() + "/" + targetEntity + "/actionSet";
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SparkAtomicActionScoreJob
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.main(
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new String[] {
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"-isSparkSessionManaged",
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Boolean.FALSE.toString(),
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"-inputPath",
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bipScoresPath,
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"-outputPath",
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workingDir.toString() + "/actionSet"
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});
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// execute the job to generate the action sets for result scores
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runJob(inputResultScores, outputPath, targetEntity);
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Result> tmp = sc
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.sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class)
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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 -> ((Result) aa.getPayload()));
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@ -140,4 +145,61 @@ public class SparkAtomicActionScoreJobTest {
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}
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@Test
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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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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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runJob(inputResultScores, outputPath, PROJECT);
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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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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// test the number of projects
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assertEquals(4, projects.count());
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String testProjectId = "40|nih_________::c02a8233e9b60f05bb418f0c9b714833";
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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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.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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// ensure that only one score is present for each bip impact measure
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assertEquals(1, m.getUnit().size());
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KeyValue kv = m.getUnit().get(0);
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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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case "numOfInfluentialResults":
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assertEquals("0", kv.getValue());
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break;
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case "numOfPopularResults":
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assertEquals("1", kv.getValue());
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break;
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case "totalImpulse":
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assertEquals("25", kv.getValue());
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break;
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case "totalCitationCount":
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assertEquals("43", kv.getValue());
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break;
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default:
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fail("Unknown measure id in the context of projects");
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}
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});
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}
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}
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@ -0,0 +1,4 @@
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{"projectId":"40|nsf_________::d93e50d22374a1cf59f6a232413ea027","numOfInfluentialResults":0,"numOfPopularResults":10,"totalImpulse":181,"totalCitationCount":235}
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{"projectId":"40|nih_________::1c93debc7085e440f245fbe70b2e8b21","numOfInfluentialResults":14,"numOfPopularResults":17,"totalImpulse":1558,"totalCitationCount":4226}
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{"projectId":"40|nih_________::c02a8233e9b60f05bb418f0c9b714833","numOfInfluentialResults":0,"numOfPopularResults":1,"totalImpulse":25,"totalCitationCount":43}
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{"projectId":"40|corda_______::d91dcf3a87dd7f72248fab0b8a4ba273","numOfInfluentialResults":2,"numOfPopularResults":3,"totalImpulse":78,"totalCitationCount":178}
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@ -96,14 +96,13 @@ for indicator_name, fd, column_name in impact_indicators:
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# print("Counting non null values for {}".format(indicator_name))
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# print(relations.filter(F.col(indicator_name).isNotNull()).count())
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sum the impact indicator values for each project
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# sum the impact indicator values for each project
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relations.groupBy('projectId')\
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.agg(\
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F.sum('influence').alias('influence'),\
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F.sum('popularity').alias('popularity'),\
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F.sum('impulse').alias('impulse'),\
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F.sum('citation_count').alias('citation_count')\
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F.sum('influence').alias('numOfInfluentialResults'),\
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F.sum('popularity').alias('numOfPopularResults'),\
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F.sum('impulse').alias('totalImpulse'),\
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F.sum('citation_count').alias('totalCitationCount')\
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)\
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.write.mode("overwrite")\
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.option("delimiter", "\t")\
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.csv(output_dir, compression="gzip")
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.json(output_dir, compression="gzip")
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