forked from D-Net/dnet-hadoop
168 lines
6.7 KiB
Java
168 lines
6.7 KiB
Java
package eu.dnetlib.dhp.oa.provision;
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import com.fasterxml.jackson.databind.ObjectMapper;
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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.oa.provision.model.*;
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import eu.dnetlib.dhp.oa.provision.utils.ContextMapper;
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import eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils;
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import eu.dnetlib.dhp.schema.oaf.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.Function;
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import org.apache.spark.api.java.function.Function2;
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import org.apache.spark.api.java.function.PairFunction;
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import org.apache.spark.rdd.RDD;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import scala.Tuple2;
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import java.io.IOException;
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import java.util.Optional;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import static eu.dnetlib.dhp.oa.provision.utils.GraphMappingUtils.*;
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/**
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* Joins the graph nodes by resolving the links of distance = 1 to create an adjacency list of linked objects.
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* The operation considers all the entity types (publication, dataset, software, ORP, project, datasource, organization,
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* and all the possible relationships (similarity links produced by the Dedup process are excluded).
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*
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* The operation is implemented by sequentially joining one entity type at time (E) with the relationships (R), and again
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* by E, finally grouped by E.id;
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*
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* The workflow is organized in different parts aimed to to reduce the complexity of the operation
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* 1) PrepareRelationsJob:
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* only consider relationships that are not virtually deleted ($.dataInfo.deletedbyinference == false), each entity
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* can be linked at most to 100 other objects
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*
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* 2) JoinRelationEntityByTargetJob:
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* prepare tuples [source entity - relation - target entity] (S - R - T):
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* for each entity type E_i
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* join (R.target = E_i.id),
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* map E_i as RelatedEntity T_i, extracting only the necessary information beforehand to produce [R - T_i]
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* join (E_i.id = [R - T_i].source), where E_i becomes the source entity S
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*
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* 3) AdjacencyListBuilderJob:
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* given the tuple (S - R - T) we need to group by S.id -> List [ R - T ], mappnig the result as JoinedEntity
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*
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* 4) XmlConverterJob:
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* convert the JoinedEntities as XML records
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*/
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public class AdjacencyListBuilderJob {
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private static final Logger log = LoggerFactory.getLogger(AdjacencyListBuilderJob.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils.toString(
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AdjacencyListBuilderJob.class
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.getResourceAsStream("/eu/dnetlib/dhp/oa/provision/input_params_build_adjacency_lists.json")));
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputPath = parser.get("inputPath");
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log.info("inputPath: {}", inputPath);
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String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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SparkConf conf = new SparkConf();
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conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
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conf.registerKryoClasses(getKryoClasses());
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runWithSparkSession(conf, isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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createAdjacencyLists(spark, inputPath, outputPath);
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});
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}
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private static void createAdjacencyLists(SparkSession spark, String inputPath, String outputPath) {
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RDD<JoinedEntity> joined = spark.read()
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.load(inputPath)
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.as(Encoders.kryo(EntityRelEntity.class))
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.javaRDD()
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.map(e -> getJoinedEntity(e))
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.mapToPair(e -> new Tuple2<>(e.getEntity().getId(), e))
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.reduceByKey((j1, j2) -> getJoinedEntity(j1, j2))
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.map(Tuple2::_2)
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.rdd();
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spark.createDataset(joined, Encoders.bean(JoinedEntity.class))
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.write()
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.mode(SaveMode.Overwrite)
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.parquet(outputPath);
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}
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private static JoinedEntity getJoinedEntity(JoinedEntity j1, JoinedEntity j2) {
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JoinedEntity je = new JoinedEntity();
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je.setEntity(je.getEntity());
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je.setType(j1.getType());
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Links links = new Links();
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links.addAll(j1.getLinks());
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links.addAll(j2.getLinks());
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return je;
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}
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private static JoinedEntity getJoinedEntity(EntityRelEntity e) {
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JoinedEntity j = new JoinedEntity();
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j.setEntity(toOafEntity(e.getEntity()));
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j.setType(EntityType.valueOf(e.getEntity().getType()));
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Links links = new Links();
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links.add(new eu.dnetlib.dhp.oa.provision.model.Tuple2(e.getRelation(), e.getTarget()));
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j.setLinks(links);
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return j;
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}
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private static OafEntity toOafEntity(TypedRow typedRow) {
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return parseOaf(typedRow.getOaf(), typedRow.getType());
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}
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private static OafEntity parseOaf(final String json, final String type) {
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try {
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switch (GraphMappingUtils.EntityType.valueOf(type)) {
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case publication:
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return OBJECT_MAPPER.readValue(json, Publication.class);
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case dataset:
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return OBJECT_MAPPER.readValue(json, Dataset.class);
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case otherresearchproduct:
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return OBJECT_MAPPER.readValue(json, OtherResearchProduct.class);
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case software:
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return OBJECT_MAPPER.readValue(json, Software.class);
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case datasource:
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return OBJECT_MAPPER.readValue(json, Datasource.class);
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case organization:
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return OBJECT_MAPPER.readValue(json, Organization.class);
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case project:
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return OBJECT_MAPPER.readValue(json, Project.class);
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default:
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throw new IllegalArgumentException("invalid type: " + type);
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}
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} catch (IOException e) {
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throw new IllegalArgumentException(e);
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}
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}
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private static void removeOutputDir(SparkSession spark, String path) {
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HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration());
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}
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}
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