forked from D-Net/dnet-hadoop
Merge actionsets of results and projects
This commit is contained in:
Serafeim Chatzopoulos
parent
3a0f09774a
commit
97c1ba8918
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@ -6,13 +6,14 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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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 org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.hadoop.mapred.SequenceFileOutputFormat;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.MapFunction;
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@ -41,8 +42,6 @@ import scala.Tuple2;
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*/
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public class SparkAtomicActionScoreJob implements Serializable {
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private static final String RESULT = "result";
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private static final String PROJECT = "project";
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private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionScoreJob.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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@ -61,15 +60,15 @@ public class SparkAtomicActionScoreJob implements Serializable {
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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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final String resultsInputPath = parser.get("resultsInputPath");
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log.info("resultsInputPath: {}", resultsInputPath);
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final String projectsInputPath = parser.get("projectsInputPath");
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log.info("projectsInputPath: {}", projectsInputPath);
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final String outputPath = parser.get("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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runWithSparkSession(
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@ -78,26 +77,23 @@ public class SparkAtomicActionScoreJob implements Serializable {
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spark -> {
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removeOutputDir(spark, outputPath);
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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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JavaPairRDD<Text, Text> resultsRDD = prepareResults(spark, resultsInputPath, outputPath);
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JavaPairRDD<Text, Text> projectsRDD = prepareProjects(spark, projectsInputPath, outputPath);
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resultsRDD
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.union(projectsRDD)
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.saveAsHadoopFile(
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outputPath, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class);
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});
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}
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private static <I extends Project> void prepareProjects(SparkSession spark, String inputPath, String outputPath) {
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private static <I extends Project> JavaPairRDD<Text, Text> prepareProjects(SparkSession spark, String inputPath,
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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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return 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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@ -107,12 +103,12 @@ public class SparkAtomicActionScoreJob implements Serializable {
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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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new Text(OBJECT_MAPPER.writeValueAsString(aa))));
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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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private static <I extends Result> JavaPairRDD<Text, Text> prepareResults(SparkSession spark, String bipScorePath,
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String outputPath) {
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final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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@ -128,24 +124,20 @@ public class SparkAtomicActionScoreJob implements Serializable {
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return bs;
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}).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class));
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bipScores
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return bipScores.map((MapFunction<BipScore, Result>) bs -> {
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Result ret = new Result();
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.map((MapFunction<BipScore, Result>) bs -> {
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Result ret = new Result();
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ret.setId(bs.getId());
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ret.setId(bs.getId());
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ret.setMeasures(getMeasure(bs));
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ret.setMeasures(getMeasure(bs));
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return ret;
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}, Encoders.bean(Result.class))
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return ret;
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}, Encoders.bean(Result.class))
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.toJavaRDD()
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.map(p -> new AtomicAction(Result.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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new Text(OBJECT_MAPPER.writeValueAsString(aa))));
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}
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private static List<Measure> getMeasure(BipScore value) {
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@ -6,9 +6,15 @@
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"paramRequired": false
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},
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{
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"paramName": "ip",
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"paramLongName": "inputPath",
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"paramDescription": "the URL from where to get the programme file",
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"paramName": "rip",
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"paramLongName": "resultsInputPath",
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"paramDescription": "the URL from where to get the input file for results",
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"paramRequired": true
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},
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{
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"paramName": "pip",
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"paramLongName": "projectsInputPath",
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"paramDescription": "the URL from where to get the input file for projects",
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"paramRequired": true
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},
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{
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@ -16,11 +22,5 @@
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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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@ -7,6 +7,8 @@ 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 javax.xml.crypto.Data;
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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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@ -27,6 +29,7 @@ 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.OafEntity;
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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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@ -38,9 +41,6 @@ public class SparkAtomicActionScoreJobTest {
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private static Path workingDir;
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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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@ -72,50 +72,64 @@ 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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private void runJob(String resultsInputPath, String projectsInputPath, String outputPath) throws Exception {
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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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"-resultsInputPath", resultsInputPath,
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"-projectsInputPath", projectsInputPath,
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"-outputPath", outputPath,
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"-targetEntity", targetEntity,
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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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String inputResultScores = getClass()
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void testScores() throws Exception {
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String resultsInputPath = 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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String projectsInputPath = 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() + "/actionSet";
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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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runJob(resultsInputPath, projectsInputPath, outputPath);
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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JavaRDD<Result> tmp = sc
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JavaRDD<OafEntity> tmp = 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 -> ((Result) aa.getPayload()));
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.map(aa -> ((OafEntity) aa.getPayload()));
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assertEquals(4, tmp.count());
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assertEquals(8, tmp.count());
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Dataset<Result> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(Result.class));
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Dataset<OafEntity> verificationDataset = spark.createDataset(tmp.rdd(), Encoders.bean(OafEntity.class));
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verificationDataset.createOrReplaceTempView("result");
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Dataset<Row> execVerification = spark
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Dataset<Row> testDataset = spark
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.sql(
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"Select p.id oaid, mes.id, mUnit.value from result p " +
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"lateral view explode(measures) m as mes " +
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"lateral view explode(mes.unit) u as mUnit ");
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Assertions.assertEquals(12, execVerification.count());
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// execVerification.show();
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Assertions.assertEquals(28, testDataset.count());
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assertResultImpactScores(testDataset);
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assertProjectImpactScores(testDataset);
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}
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void assertResultImpactScores(Dataset<Row> testDataset) {
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Assertions
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.assertEquals(
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"6.63451994567e-09", execVerification
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"6.63451994567e-09", testDataset
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.filter(
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"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
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"and id = 'influence'")
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@ -125,7 +139,7 @@ public class SparkAtomicActionScoreJobTest {
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.getString(0));
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Assertions
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.assertEquals(
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"0.348694533145", execVerification
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"0.348694533145", testDataset
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.filter(
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"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
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"and id = 'popularity_alt'")
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@ -135,7 +149,7 @@ public class SparkAtomicActionScoreJobTest {
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.getString(0));
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Assertions
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.assertEquals(
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"2.16094680115e-09", execVerification
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"2.16094680115e-09", testDataset
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.filter(
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"oaid='50|arXiv_dedup_::4a2d5fd8d71daec016c176ec71d957b1' " +
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"and id = 'popularity'")
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@ -143,65 +157,49 @@ public class SparkAtomicActionScoreJobTest {
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.collectAsList()
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.get(0)
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.getString(0));
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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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void assertProjectImpactScores(Dataset<Row> testDataset) throws Exception {
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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
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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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// 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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Assertions
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.assertEquals(
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"0", testDataset
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.filter(
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"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
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"and id = 'numOfInfluentialResults'")
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.select("value")
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.collectAsList()
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.get(0)
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.getString(0));
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Assertions
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.assertEquals(
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"1", testDataset
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.filter(
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"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
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"and id = 'numOfPopularResults'")
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.select("value")
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.collectAsList()
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.get(0)
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.getString(0));
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Assertions
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.assertEquals(
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"25", testDataset
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.filter(
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"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
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"and id = 'totalImpulse'")
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.select("value")
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.collectAsList()
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.get(0)
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.getString(0));
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Assertions
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.assertEquals(
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"43", testDataset
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.filter(
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"oaid='40|nih_________::c02a8233e9b60f05bb418f0c9b714833' " +
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"and id = 'totalCitationCount'")
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.select("value")
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.collectAsList()
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.get(0)
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.getString(0));
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}
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}
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@ -31,7 +31,7 @@
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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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<case to="create-actionset">${wf:conf('resume') eq "create-actionset"}</case>
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<default to="create-openaire-ranking-graph" />
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</switch>
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@ -455,53 +455,11 @@
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<file>${wfAppPath}/map_scores_to_dois.py#map_scores_to_dois.py</file>
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</spark>
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<ok to="delete-output-path-for-actionset" />
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<ok to="project-impact-indicators" />
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<error to="map-scores-fail" />
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</action>
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<!-- Re-create folder for result and project actionsets -->
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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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<mkdir path="${actionSetOutputPath}/results/"/>
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<mkdir path="${actionSetOutputPath}/projects/"/>
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</fs>
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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="create-actionset-for-results">
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<spark xmlns="uri:oozie:spark-action:0.2">
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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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<jar>dhp-aggregation-${projectVersion}.jar</jar>
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<spark-opts>
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--executor-memory=${sparkNormalExecutorMemory}
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--executor-cores=${sparkExecutorCores}
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--driver-memory=${sparkNormalDriverMemory}
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--conf spark.extraListeners=${spark2ExtraListeners}
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--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
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--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
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--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
<arg>--inputPath</arg><arg>${bipScorePath}</arg>
|
||||
<arg>--outputPath</arg><arg>${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">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
|
||||
|
|
@ -538,17 +496,26 @@
|
|||
<file>${wfAppPath}/projects_impact.py#projects_impact.py</file>
|
||||
</spark>
|
||||
|
||||
<ok to="create-actionset-for-projects" />
|
||||
<ok to="delete-output-path-for-actionset" />
|
||||
<error to="project-impact-indicators-fail" />
|
||||
|
||||
</action>
|
||||
|
||||
<action name="create-actionset-for-projects">
|
||||
<!-- Re-create folder for actionsets -->
|
||||
<action name="delete-output-path-for-actionset">
|
||||
<fs>
|
||||
<delete path="${actionSetOutputPath}"/>
|
||||
<mkdir path="${actionSetOutputPath}"/>
|
||||
</fs>
|
||||
<ok to="create-actionset"/>
|
||||
<error to="actionset-delete-fail"/>
|
||||
</action>
|
||||
|
||||
<action name="create-actionset">
|
||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||
|
||||
<master>yarn-cluster</master>
|
||||
<mode>cluster</mode>
|
||||
<name>Produces the atomic action with the bip finder scores for projects</name>
|
||||
<name>Produces the atomic action with the bip finder scores</name>
|
||||
<class>eu.dnetlib.dhp.actionmanager.bipfinder.SparkAtomicActionScoreJob</class>
|
||||
<jar>dhp-aggregation-${projectVersion}.jar</jar>
|
||||
|
||||
|
|
@ -563,14 +530,13 @@
|
|||
--conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir}
|
||||
</spark-opts>
|
||||
|
||||
<arg>--inputPath</arg><arg>${projectImpactIndicatorsOutput}</arg>
|
||||
<arg>--outputPath</arg><arg>${actionSetOutputPath}/projects/</arg>
|
||||
<arg>--targetEntity</arg><arg>project</arg>
|
||||
<arg>--resultsInputPath</arg><arg>${bipScorePath}</arg>
|
||||
<arg>--projectsInputPath</arg><arg>${projectImpactIndicatorsOutput}</arg>
|
||||
<arg>--outputPath</arg><arg>${actionSetOutputPath}</arg>
|
||||
</spark>
|
||||
|
||||
<ok to="end"/>
|
||||
<error to="actionset-project-creation-fail"/>
|
||||
|
||||
<error to="actionset-creation-fail"/>
|
||||
</action>
|
||||
|
||||
<!-- Definitions of failure messages -->
|
||||
|
|
@ -630,10 +596,6 @@
|
|||
<message>Calculating project impact indicators failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<kill name="actionset-project-creation-fail">
|
||||
<message>ActionSet creation for projects failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||
</kill>
|
||||
|
||||
<!-- Define ending node -->
|
||||
<end name="end" />
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue