forked from D-Net/dnet-hadoop
implemented Creation of Raw Graph and Resolution
This commit is contained in:
parent
623a0c4edb
commit
1a6b398968
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package eu.dnetlib.dhp.sx.graph
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case class IdReplace(newId:String, oldId:String) {}
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@ -1,153 +0,0 @@
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package eu.dnetlib.dhp.sx.graph;
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import java.io.IOException;
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import java.net.URI;
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import java.util.ArrayList;
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import java.util.List;
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import java.util.Objects;
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import java.util.concurrent.atomic.AtomicInteger;
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import java.util.function.Consumer;
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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.conf.Configuration;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.fs.Path;
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import org.apache.hadoop.io.IntWritable;
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import org.apache.hadoop.io.SequenceFile;
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import org.apache.hadoop.io.Text;
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import org.bson.Document;
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import org.bson.conversions.Bson;
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import com.mongodb.DBObject;
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import com.mongodb.MongoClient;
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import com.mongodb.QueryBuilder;
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import com.mongodb.client.FindIterable;
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import com.mongodb.client.MongoCollection;
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import com.mongodb.client.MongoDatabase;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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/**
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* This job is responsible to collect data from mongoDatabase and store in a sequence File on HDFS Mongo database
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* contains information of each MDSTore in two collections: -metadata That contains info like: ID, format, layout,
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* interpretation -metadataManager: that contains info : ID, mongoCollectionName from the metadata collection we filter
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* the ids with Format, layout, and Interpretation from the metadataManager we get the current MONGO collection name
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* which contains metadata XML see function getCurrentId
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* <p>
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* This Job will be called different times in base at the triple we want import, and generates for each triple a
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* sequence file of XML
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*/
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public class ImportDataFromMongo {
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/**
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* It requires in input some parameters described on a file
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* eu/dnetlib/dhp/graph/sx/import_from_mongo_parameters.json
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* <p>
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* - the name node - the paht where store HDFS File - the mongo host - the mongo port - the metadata format to
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* import - the metadata layout to import - the metadata interpretation to import - the mongo database Name
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* <p>
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* This params are encoded into args
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*
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* @param args
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* @throws Exception
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*/
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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
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.toString(
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ImportDataFromMongo.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/sx/graph/argumentparser/import_from_mongo_parameters.json")));
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parser.parseArgument(args);
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final int port = Integer.parseInt(parser.get("dbport"));
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final String host = parser.get("dbhost");
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final String format = parser.get("format");
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final String layout = parser.get("layout");
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final String interpretation = parser.get("interpretation");
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final String dbName = parser.get("dbName");
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final MongoClient client = new MongoClient(host, port);
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MongoDatabase database = client.getDatabase(dbName);
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MongoCollection<Document> metadata = database.getCollection("metadata");
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MongoCollection<Document> metadataManager = database.getCollection("metadataManager");
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final DBObject query = QueryBuilder
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.start("format")
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.is(format)
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.and("layout")
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.is(layout)
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.and("interpretation")
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.is(interpretation)
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.get();
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final List<String> ids = new ArrayList<>();
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metadata
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.find((Bson) query)
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.forEach((Consumer<Document>) document -> ids.add(document.getString("mdId")));
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List<String> databaseId = ids
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.stream()
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.map(it -> getCurrentId(it, metadataManager))
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.filter(Objects::nonNull)
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.collect(Collectors.toList());
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final String hdfsuri = parser.get("namenode");
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// ====== Init HDFS File System Object
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Configuration conf = new Configuration();
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// Set FileSystem URI
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conf.set("fs.defaultFS", hdfsuri);
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// Because of Maven
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conf.set("fs.hdfs.impl", org.apache.hadoop.hdfs.DistributedFileSystem.class.getName());
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conf.set("fs.file.impl", org.apache.hadoop.fs.LocalFileSystem.class.getName());
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FileSystem.get(URI.create(hdfsuri), conf);
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Path hdfswritepath = new Path(parser.get("targetPath"));
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final AtomicInteger counter = new AtomicInteger(0);
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try (SequenceFile.Writer writer = SequenceFile
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.createWriter(
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conf,
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SequenceFile.Writer.file(hdfswritepath),
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SequenceFile.Writer.keyClass(IntWritable.class),
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SequenceFile.Writer.valueClass(Text.class))) {
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final IntWritable key = new IntWritable(counter.get());
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final Text value = new Text();
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databaseId
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.forEach(
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id -> {
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System.out.println("Reading :" + id);
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MongoCollection<Document> collection = database.getCollection(id);
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collection
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.find()
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.forEach(
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(Consumer<Document>) document -> {
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key.set(counter.getAndIncrement());
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value.set(document.getString("body"));
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if (counter.get() % 10000 == 0) {
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System.out.println("Added " + counter.get());
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}
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try {
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writer.append(key, value);
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} catch (IOException e) {
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throw new RuntimeException(e);
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}
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});
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});
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}
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}
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/**
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* Return the name of mongo collection giving an MdStore ID
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*
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* @param mdId The id of the MDStore
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* @param metadataManager The collection metadataManager on mongo which contains this information
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* @return
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*/
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private static String getCurrentId(
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final String mdId, final MongoCollection<Document> metadataManager) {
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FindIterable<Document> result = metadataManager.find((Bson) QueryBuilder.start("mdId").is(mdId).get());
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final Document item = result.first();
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return item == null ? null : item.getString("currentId");
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}
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}
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package eu.dnetlib.dhp.sx.graph
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import eu.dnetlib.dhp.application.ArgumentApplicationParser
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import eu.dnetlib.dhp.schema.oaf.{Oaf, OtherResearchProduct, Publication, Relation, Result, Software, Dataset => OafDataset}
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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.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
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import org.slf4j.{Logger, LoggerFactory}
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object SparkCreateInputGraph {
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def main(args: Array[String]): Unit = {
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val log: Logger = LoggerFactory.getLogger(getClass)
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val conf: SparkConf = new SparkConf()
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val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/extract_entities_params.json")))
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parser.parseArgument(args)
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val spark: SparkSession =
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SparkSession
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.builder()
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.config(conf)
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.appName(getClass.getSimpleName)
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.master(parser.get("master")).getOrCreate()
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val resultObject = List(
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("publication", classOf[Publication]),
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("dataset", classOf[OafDataset]),
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("software", classOf[Software]),
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("otherResearchProduct", classOf[OtherResearchProduct])
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)
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implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf])
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val sourcePath = parser.get("sourcePath")
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log.info(s"sourcePath -> $sourcePath")
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val targetPath = parser.get("targetPath")
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log.info(s"targetPath -> $targetPath")
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val oafDs:Dataset[Oaf] = spark.read.load(s"$sourcePath/*").as[Oaf]
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resultObject.foreach(r => extractEntities(oafDs,s"$targetPath/extracted/${r._1}", r._2, log))
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extractEntities(oafDs,s"$targetPath/extracted/relation", classOf[Relation], log)
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resultObject.foreach { r =>
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log.info(s"Make ${r._1} unique")
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makeDatasetUnique(s"$targetPath/extracted/${r._1}",s"$targetPath/dedup/${r._1}",spark, r._2)
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}
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}
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def extractEntities[T <: Oaf ](oafDs:Dataset[Oaf], targetPath:String, clazz:Class[T], log:Logger) :Unit = {
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implicit val resEncoder: Encoder[T] = Encoders.kryo(clazz)
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log.info(s"Extract ${clazz.getSimpleName}")
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oafDs.filter(o => o.isInstanceOf[T]).map(p => p.asInstanceOf[T]).write.mode(SaveMode.Overwrite).save(targetPath)
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}
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def makeDatasetUnique[T <: Result ](sourcePath:String, targetPath:String, spark:SparkSession, clazz:Class[T]) :Unit = {
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import spark.implicits._
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implicit val resEncoder: Encoder[T] = Encoders.kryo(clazz)
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val ds:Dataset[T] = spark.read.load(sourcePath).as[T]
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ds.groupByKey(_.getId).reduceGroups{(x,y) =>
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x.mergeFrom(y)
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x
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}.map(_._2).write.mode(SaveMode.Overwrite).save(targetPath)
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}
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}
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package eu.dnetlib.dhp.sx.graph;
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import java.util.Arrays;
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import java.util.List;
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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.commons.lang3.StringUtils;
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import org.apache.hadoop.io.compress.GzipCodec;
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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.sql.SparkSession;
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import com.jayway.jsonpath.JsonPath;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import net.minidev.json.JSONArray;
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/**
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* This Job extracts a typology of entity and stores it in a new RDD This job is called different times, for each file
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* generated by the Job {@link ImportDataFromMongo} and store the new RDD in a path that should be under a folder:
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* extractedEntities/entity/version1
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* <p>
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* at the end of this process we will have : extractedEntities/dataset/version1 extractedEntities/dataset/version2
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* extractedEntities/dataset/... extractedEntities/publication/version1 extractedEntities/publication/version2
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* extractedEntities/publication/... extractedEntities/unknown/version1 extractedEntities/unknown/version2
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* extractedEntities/unknown/... extractedEntities/relation/version1 extractedEntities/relation/version2
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* extractedEntities/relation/...
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*/
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public class SparkExtractEntitiesJob {
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static final String IDJSONPATH = "$.id";
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static final String SOURCEJSONPATH = "$.source";
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static final String TARGETJSONPATH = "$.target";
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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
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.toString(
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SparkExtractEntitiesJob.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json")));
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parser.parseArgument(args);
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final SparkSession spark = SparkSession
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.builder()
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.appName(SparkExtractEntitiesJob.class.getSimpleName())
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.master(parser.get("master"))
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.getOrCreate();
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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final String inputPath = parser.get("sourcePath");
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final String targetPath = parser.get("targetPath");
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final String tdir = parser.get("targetDir");
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final JavaRDD<String> inputRDD = sc.textFile(inputPath);
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List<String> entities = Arrays
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.stream(parser.get("entities").split(","))
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.map(String::trim)
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.collect(Collectors.toList());
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if (entities.stream().anyMatch("dataset"::equalsIgnoreCase)) {
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// Extract Dataset
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inputRDD
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.filter(SparkExtractEntitiesJob::isDataset)
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.saveAsTextFile(targetPath + "/dataset/" + tdir, GzipCodec.class);
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}
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if (entities.stream().anyMatch("unknown"::equalsIgnoreCase)) {
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// Extract Unknown
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inputRDD
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.filter(SparkExtractEntitiesJob::isUnknown)
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.saveAsTextFile(targetPath + "/unknown/" + tdir, GzipCodec.class);
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}
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if (entities.stream().anyMatch("relation"::equalsIgnoreCase)) {
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// Extract Relation
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inputRDD
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.filter(SparkExtractEntitiesJob::isRelation)
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.saveAsTextFile(targetPath + "/relation/" + tdir, GzipCodec.class);
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}
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if (entities.stream().anyMatch("publication"::equalsIgnoreCase)) {
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// Extract Relation
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inputRDD
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.filter(SparkExtractEntitiesJob::isPublication)
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.saveAsTextFile(targetPath + "/publication/" + tdir, GzipCodec.class);
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}
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}
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public static boolean isDataset(final String json) {
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final String id = getJPathString(IDJSONPATH, json);
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if (StringUtils.isBlank(id))
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return false;
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return id.startsWith("60|");
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}
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public static boolean isPublication(final String json) {
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final String id = getJPathString(IDJSONPATH, json);
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if (StringUtils.isBlank(id))
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return false;
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return id.startsWith("50|");
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}
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public static boolean isUnknown(final String json) {
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final String id = getJPathString(IDJSONPATH, json);
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if (StringUtils.isBlank(id))
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return false;
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return id.startsWith("70|");
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}
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public static boolean isRelation(final String json) {
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final String source = getJPathString(SOURCEJSONPATH, json);
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final String target = getJPathString(TARGETJSONPATH, json);
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return StringUtils.isNotBlank(source) && StringUtils.isNotBlank(target);
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}
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public static String getJPathString(final String jsonPath, final String json) {
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try {
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Object o = JsonPath.read(json, jsonPath);
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if (o instanceof String)
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return (String) o;
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if (o instanceof JSONArray && ((JSONArray) o).size() > 0)
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return (String) ((JSONArray) o).get(0);
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return "";
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} catch (Exception e) {
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return "";
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}
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}
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}
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@ -0,0 +1,90 @@
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package eu.dnetlib.dhp.sx.graph
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|
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.{Relation, Result}
|
||||||
|
import org.apache.commons.io.IOUtils
|
||||||
|
import org.apache.spark.SparkConf
|
||||||
|
import org.apache.spark.sql._
|
||||||
|
import org.slf4j.{Logger, LoggerFactory}
|
||||||
|
|
||||||
|
import scala.collection.JavaConverters._
|
||||||
|
object SparkResolveRelation {
|
||||||
|
def main(args: Array[String]): Unit = {
|
||||||
|
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||||
|
val conf: SparkConf = new SparkConf()
|
||||||
|
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/resolve_relations_params.json")))
|
||||||
|
parser.parseArgument(args)
|
||||||
|
val spark: SparkSession =
|
||||||
|
SparkSession
|
||||||
|
.builder()
|
||||||
|
.config(conf)
|
||||||
|
.appName(getClass.getSimpleName)
|
||||||
|
.master(parser.get("master")).getOrCreate()
|
||||||
|
|
||||||
|
|
||||||
|
val relationPath = parser.get("relationPath")
|
||||||
|
log.info(s"sourcePath -> $relationPath")
|
||||||
|
val entityPath = parser.get("entityPath")
|
||||||
|
log.info(s"targetPath -> $entityPath")
|
||||||
|
val workingPath = parser.get("workingPath")
|
||||||
|
log.info(s"workingPath -> $workingPath")
|
||||||
|
|
||||||
|
|
||||||
|
implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result])
|
||||||
|
implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation])
|
||||||
|
import spark.implicits._
|
||||||
|
val entities:Dataset[Result] = spark.read.load(s"$entityPath/*").as[Result]
|
||||||
|
|
||||||
|
entities.flatMap(e => e.getPid.asScala
|
||||||
|
.map(p =>
|
||||||
|
convertPidToDNETIdentifier(p.getValue, p.getQualifier.getClassid))
|
||||||
|
.filter(s => s!= null)
|
||||||
|
.map(s => (s,e.getId))
|
||||||
|
).groupByKey(_._1)
|
||||||
|
.reduceGroups((x,y) => if (x._2.startsWith("50|doi") || x._2.startsWith("50|pmid")) x else y)
|
||||||
|
.map(s =>s._2)
|
||||||
|
.write
|
||||||
|
.mode(SaveMode.Overwrite)
|
||||||
|
.save(s"$workingPath/resolvedPid")
|
||||||
|
|
||||||
|
val rPid:Dataset[(String,String)] = spark.read.load(s"$workingPath/resolvedPid").as[(String,String)]
|
||||||
|
|
||||||
|
val relationDs:Dataset[(String,Relation)] = spark.read.load(relationPath).as[Relation].map(r => (r.getSource.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
|
||||||
|
|
||||||
|
relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_1")), "left").map{
|
||||||
|
m =>
|
||||||
|
val sourceResolved = m._2
|
||||||
|
val currentRelation = m._1._2
|
||||||
|
if (sourceResolved!=null && sourceResolved._2.nonEmpty)
|
||||||
|
currentRelation.setSource(sourceResolved._2)
|
||||||
|
currentRelation
|
||||||
|
}.write
|
||||||
|
.mode(SaveMode.Overwrite)
|
||||||
|
.save(s"$workingPath/resolvedSource")
|
||||||
|
|
||||||
|
|
||||||
|
val relationSourceResolved:Dataset[(String,Relation)] = spark.read.load(s"$workingPath/resolvedSource").as[Relation].map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder))
|
||||||
|
relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_1")), "left").map{
|
||||||
|
m =>
|
||||||
|
val targetResolved = m._2
|
||||||
|
val currentRelation = m._1._2
|
||||||
|
if (targetResolved!=null && targetResolved._2.nonEmpty)
|
||||||
|
currentRelation.setTarget(targetResolved._2)
|
||||||
|
currentRelation
|
||||||
|
}.filter(r => r.getSource.startsWith("50")&& r.getTarget.startsWith("50"))
|
||||||
|
.write
|
||||||
|
.mode(SaveMode.Overwrite)
|
||||||
|
.save(s"$workingPath/resolvedRelation")
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
def convertPidToDNETIdentifier(pid:String, pidType: String):String = {
|
||||||
|
if (pid==null || pid.isEmpty || pidType== null || pidType.isEmpty)
|
||||||
|
null
|
||||||
|
else
|
||||||
|
s"unresolved::${pid.toLowerCase}::${pidType.toLowerCase}"
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -1,75 +0,0 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.sx.graph;
|
|
||||||
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
|
||||||
import org.apache.spark.api.java.JavaPairRDD;
|
|
||||||
import org.apache.spark.api.java.JavaRDD;
|
|
||||||
import org.apache.spark.api.java.JavaSparkContext;
|
|
||||||
import org.apache.spark.api.java.function.PairFunction;
|
|
||||||
import org.apache.spark.sql.Encoders;
|
|
||||||
import org.apache.spark.sql.SaveMode;
|
|
||||||
import org.apache.spark.sql.SparkSession;
|
|
||||||
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
||||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
|
||||||
import scala.Tuple2;
|
|
||||||
|
|
||||||
/**
|
|
||||||
* In some case the identifier generated for the Entity in @{@link SparkExtractEntitiesJob} is different from the
|
|
||||||
* identifier * associated by the aggregator, this means that some relation points to missing identifier To avoid this
|
|
||||||
* problem we store in the model the Id and the OriginalObJIdentifier This jobs extract this pair and creates a Similar
|
|
||||||
* relation that will be used in SparkMergeEntities
|
|
||||||
*/
|
|
||||||
public class SparkSXGeneratePidSimlarity {
|
|
||||||
|
|
||||||
static final String IDJSONPATH = "$.id";
|
|
||||||
static final String OBJIDPATH = "$.originalObjIdentifier";
|
|
||||||
|
|
||||||
public static void generateDataFrame(
|
|
||||||
final SparkSession spark,
|
|
||||||
final JavaSparkContext sc,
|
|
||||||
final String inputPath,
|
|
||||||
final String targetPath) {
|
|
||||||
|
|
||||||
final JavaPairRDD<String, String> datasetSimRel = sc
|
|
||||||
.textFile(inputPath + "/dataset/*")
|
|
||||||
.mapToPair(
|
|
||||||
(PairFunction<String, String, String>) k -> new Tuple2<>(
|
|
||||||
DHPUtils.getJPathString(IDJSONPATH, k),
|
|
||||||
DHPUtils.getJPathString(OBJIDPATH, k)))
|
|
||||||
.filter(
|
|
||||||
t -> !StringUtils
|
|
||||||
.substringAfter(t._1(), "|")
|
|
||||||
.equalsIgnoreCase(StringUtils.substringAfter(t._2(), "::")))
|
|
||||||
.distinct();
|
|
||||||
|
|
||||||
final JavaPairRDD<String, String> publicationSimRel = sc
|
|
||||||
.textFile(inputPath + "/publication/*")
|
|
||||||
.mapToPair(
|
|
||||||
(PairFunction<String, String, String>) k -> new Tuple2<>(
|
|
||||||
DHPUtils.getJPathString(IDJSONPATH, k),
|
|
||||||
DHPUtils.getJPathString(OBJIDPATH, k)))
|
|
||||||
.filter(
|
|
||||||
t -> !StringUtils
|
|
||||||
.substringAfter(t._1(), "|")
|
|
||||||
.equalsIgnoreCase(StringUtils.substringAfter(t._2(), "::")))
|
|
||||||
.distinct();
|
|
||||||
|
|
||||||
JavaRDD<Relation> simRel = datasetSimRel
|
|
||||||
.union(publicationSimRel)
|
|
||||||
.map(
|
|
||||||
s -> {
|
|
||||||
final Relation r = new Relation();
|
|
||||||
r.setSource(s._1());
|
|
||||||
r.setTarget(s._2());
|
|
||||||
r.setRelType("similar");
|
|
||||||
return r;
|
|
||||||
});
|
|
||||||
spark
|
|
||||||
.createDataset(simRel.rdd(), Encoders.bean(Relation.class))
|
|
||||||
.distinct()
|
|
||||||
.write()
|
|
||||||
.mode(SaveMode.Overwrite)
|
|
||||||
.save(targetPath + "/pid_simRel");
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,256 +0,0 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.sx.graph;
|
|
||||||
|
|
||||||
import java.util.ArrayList;
|
|
||||||
import java.util.Arrays;
|
|
||||||
import java.util.List;
|
|
||||||
import java.util.stream.Collectors;
|
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
|
||||||
import org.apache.commons.lang3.StringUtils;
|
|
||||||
import org.apache.hadoop.fs.FileStatus;
|
|
||||||
import org.apache.hadoop.fs.FileSystem;
|
|
||||||
import org.apache.hadoop.fs.Path;
|
|
||||||
import org.apache.hadoop.io.compress.GzipCodec;
|
|
||||||
import org.apache.spark.SparkConf;
|
|
||||||
import org.apache.spark.api.java.JavaRDD;
|
|
||||||
import org.apache.spark.api.java.JavaSparkContext;
|
|
||||||
import org.apache.spark.api.java.function.MapFunction;
|
|
||||||
import org.apache.spark.api.java.function.PairFunction;
|
|
||||||
import org.apache.spark.rdd.RDD;
|
|
||||||
import org.apache.spark.sql.Dataset;
|
|
||||||
import org.apache.spark.sql.Encoders;
|
|
||||||
import org.apache.spark.sql.SaveMode;
|
|
||||||
import org.apache.spark.sql.SparkSession;
|
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.DeserializationFeature;
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import com.jayway.jsonpath.JsonPath;
|
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
||||||
import eu.dnetlib.dhp.schema.scholexplorer.DLIDataset;
|
|
||||||
import eu.dnetlib.dhp.schema.scholexplorer.DLIPublication;
|
|
||||||
import eu.dnetlib.dhp.schema.scholexplorer.DLIUnknown;
|
|
||||||
import eu.dnetlib.dhp.utils.DHPUtils;
|
|
||||||
import net.minidev.json.JSONArray;
|
|
||||||
import scala.Tuple2;
|
|
||||||
|
|
||||||
/**
|
|
||||||
* This job is responsible of the creation of RAW Graph It is applied to the different entities generated from
|
|
||||||
* {@link SparkExtractEntitiesJob} In case of dataset, publication and Unknown Entities we group all the entities of the
|
|
||||||
* same type by their identifier, and then in the reduce phase we merge all the entities. Merge means: -merge all the
|
|
||||||
* metadata -merge the collected From values
|
|
||||||
* <p>
|
|
||||||
* In case of relation we need to make a different work: -Phase 1: Map reduce jobs Map: Get all Relation and emit a key
|
|
||||||
* constructed by (source, relType, Target) and the relation itself Reduce: Merge all relations Looking at the javadoc
|
|
||||||
* of {@link SparkSXGeneratePidSimlarity} we take the dataset of pid relation and joining by source and target we
|
|
||||||
* replace the wrong identifier in the relation with the correct ones. At the end we replace the new Dataset of Relation
|
|
||||||
*/
|
|
||||||
public class SparkScholexplorerCreateRawGraphJob {
|
|
||||||
|
|
||||||
static final String IDJSONPATH = "$.id";
|
|
||||||
static final String SOURCEJSONPATH = "$.source";
|
|
||||||
static final String TARGETJSONPATH = "$.target";
|
|
||||||
static final String RELJSONPATH = "$.relType";
|
|
||||||
|
|
||||||
public static void main(String[] args) throws Exception {
|
|
||||||
|
|
||||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
|
||||||
IOUtils
|
|
||||||
.toString(
|
|
||||||
SparkScholexplorerCreateRawGraphJob.class
|
|
||||||
.getResourceAsStream(
|
|
||||||
"/eu/dnetlib/dhp/sx/graph/argumentparser/merge_entities_scholix_parameters.json")));
|
|
||||||
parser.parseArgument(args);
|
|
||||||
final SparkSession spark = SparkSession
|
|
||||||
.builder()
|
|
||||||
.config(
|
|
||||||
new SparkConf()
|
|
||||||
.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"))
|
|
||||||
.appName(SparkScholexplorerCreateRawGraphJob.class.getSimpleName())
|
|
||||||
.master(parser.get("master"))
|
|
||||||
.getOrCreate();
|
|
||||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
|
||||||
final String inputPath = parser.get("sourcePath");
|
|
||||||
final String targetPath = parser.get("targetPath");
|
|
||||||
final String entity = parser.get("entity");
|
|
||||||
FileSystem fs = FileSystem.get(sc.sc().hadoopConfiguration());
|
|
||||||
List<Path> subFolder = Arrays
|
|
||||||
.stream(fs.listStatus(new Path(inputPath)))
|
|
||||||
.filter(FileStatus::isDirectory)
|
|
||||||
.map(FileStatus::getPath)
|
|
||||||
.collect(Collectors.toList());
|
|
||||||
List<JavaRDD<String>> inputRdd = new ArrayList<>();
|
|
||||||
subFolder.forEach(p -> inputRdd.add(sc.textFile(p.toUri().getRawPath())));
|
|
||||||
JavaRDD<String> union = sc.emptyRDD();
|
|
||||||
for (JavaRDD<String> item : inputRdd) {
|
|
||||||
union = union.union(item);
|
|
||||||
}
|
|
||||||
switch (entity) {
|
|
||||||
case "dataset":
|
|
||||||
union
|
|
||||||
.mapToPair(
|
|
||||||
(PairFunction<String, String, DLIDataset>) f -> {
|
|
||||||
final String id = getJPathString(IDJSONPATH, f);
|
|
||||||
ObjectMapper mapper = new ObjectMapper();
|
|
||||||
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
|
||||||
return new Tuple2<>(id, mapper.readValue(f, DLIDataset.class));
|
|
||||||
})
|
|
||||||
.reduceByKey(
|
|
||||||
(a, b) -> {
|
|
||||||
a.mergeFrom(b);
|
|
||||||
return a;
|
|
||||||
})
|
|
||||||
.map(
|
|
||||||
item -> {
|
|
||||||
ObjectMapper mapper = new ObjectMapper();
|
|
||||||
return mapper.writeValueAsString(item._2());
|
|
||||||
})
|
|
||||||
.saveAsTextFile(targetPath, GzipCodec.class);
|
|
||||||
break;
|
|
||||||
case "publication":
|
|
||||||
union
|
|
||||||
.mapToPair(
|
|
||||||
(PairFunction<String, String, DLIPublication>) f -> {
|
|
||||||
final String id = getJPathString(IDJSONPATH, f);
|
|
||||||
ObjectMapper mapper = new ObjectMapper();
|
|
||||||
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
|
||||||
return new Tuple2<>(id, mapper.readValue(f, DLIPublication.class));
|
|
||||||
})
|
|
||||||
.reduceByKey(
|
|
||||||
(a, b) -> {
|
|
||||||
a.mergeFrom(b);
|
|
||||||
return a;
|
|
||||||
})
|
|
||||||
.map(
|
|
||||||
item -> {
|
|
||||||
ObjectMapper mapper = new ObjectMapper();
|
|
||||||
return mapper.writeValueAsString(item._2());
|
|
||||||
})
|
|
||||||
.saveAsTextFile(targetPath, GzipCodec.class);
|
|
||||||
break;
|
|
||||||
case "unknown":
|
|
||||||
union
|
|
||||||
.mapToPair(
|
|
||||||
(PairFunction<String, String, DLIUnknown>) f -> {
|
|
||||||
final String id = getJPathString(IDJSONPATH, f);
|
|
||||||
ObjectMapper mapper = new ObjectMapper();
|
|
||||||
mapper.configure(DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
|
||||||
return new Tuple2<>(id, mapper.readValue(f, DLIUnknown.class));
|
|
||||||
})
|
|
||||||
.reduceByKey(
|
|
||||||
(a, b) -> {
|
|
||||||
a.mergeFrom(b);
|
|
||||||
return a;
|
|
||||||
})
|
|
||||||
.map(
|
|
||||||
item -> {
|
|
||||||
ObjectMapper mapper = new ObjectMapper();
|
|
||||||
return mapper.writeValueAsString(item._2());
|
|
||||||
})
|
|
||||||
.saveAsTextFile(targetPath, GzipCodec.class);
|
|
||||||
break;
|
|
||||||
case "relation":
|
|
||||||
SparkSXGeneratePidSimlarity
|
|
||||||
.generateDataFrame(
|
|
||||||
spark, sc, inputPath.replace("/relation", ""), targetPath.replace("/relation", ""));
|
|
||||||
RDD<Relation> rdd = union
|
|
||||||
.mapToPair(
|
|
||||||
(PairFunction<String, String, Relation>) f -> {
|
|
||||||
final String source = getJPathString(SOURCEJSONPATH, f);
|
|
||||||
final String target = getJPathString(TARGETJSONPATH, f);
|
|
||||||
final String reltype = getJPathString(RELJSONPATH, f);
|
|
||||||
ObjectMapper mapper = new ObjectMapper();
|
|
||||||
mapper
|
|
||||||
.configure(
|
|
||||||
DeserializationFeature.FAIL_ON_UNKNOWN_PROPERTIES, false);
|
|
||||||
return new Tuple2<>(
|
|
||||||
DHPUtils
|
|
||||||
.md5(
|
|
||||||
String
|
|
||||||
.format(
|
|
||||||
"%s::%s::%s",
|
|
||||||
source.toLowerCase(),
|
|
||||||
reltype.toLowerCase(),
|
|
||||||
target.toLowerCase())),
|
|
||||||
mapper.readValue(f, Relation.class));
|
|
||||||
})
|
|
||||||
.reduceByKey(
|
|
||||||
(a, b) -> {
|
|
||||||
a.mergeFrom(b);
|
|
||||||
return a;
|
|
||||||
})
|
|
||||||
.map(Tuple2::_2)
|
|
||||||
.rdd();
|
|
||||||
|
|
||||||
spark
|
|
||||||
.createDataset(rdd, Encoders.bean(Relation.class))
|
|
||||||
.write()
|
|
||||||
.mode(SaveMode.Overwrite)
|
|
||||||
.save(targetPath);
|
|
||||||
Dataset<Relation> rel_ds = spark.read().load(targetPath).as(Encoders.bean(Relation.class));
|
|
||||||
|
|
||||||
System.out.println("LOADING PATH :" + targetPath.replace("/relation", "") + "/pid_simRel");
|
|
||||||
Dataset<Relation> sim_ds = spark
|
|
||||||
.read()
|
|
||||||
.load(targetPath.replace("/relation", "") + "/pid_simRel")
|
|
||||||
.as(Encoders.bean(Relation.class));
|
|
||||||
|
|
||||||
Dataset<Relation> ids = sim_ds
|
|
||||||
.map(
|
|
||||||
(MapFunction<Relation, Relation>) relation -> {
|
|
||||||
final String type = StringUtils.substringBefore(relation.getSource(), "|");
|
|
||||||
relation
|
|
||||||
.setTarget(
|
|
||||||
String
|
|
||||||
.format(
|
|
||||||
"%s|%s",
|
|
||||||
type, StringUtils.substringAfter(relation.getTarget(), "::")));
|
|
||||||
return relation;
|
|
||||||
},
|
|
||||||
Encoders.bean(Relation.class));
|
|
||||||
|
|
||||||
final Dataset<Relation> firstJoin = rel_ds
|
|
||||||
.joinWith(ids, ids.col("target").equalTo(rel_ds.col("source")), "left_outer")
|
|
||||||
.map(
|
|
||||||
(MapFunction<Tuple2<Relation, Relation>, Relation>) s -> {
|
|
||||||
if (s._2() != null) {
|
|
||||||
s._1().setSource(s._2().getSource());
|
|
||||||
}
|
|
||||||
return s._1();
|
|
||||||
},
|
|
||||||
Encoders.bean(Relation.class));
|
|
||||||
|
|
||||||
Dataset<Relation> secondJoin = firstJoin
|
|
||||||
.joinWith(ids, ids.col("target").equalTo(firstJoin.col("target")), "left_outer")
|
|
||||||
.map(
|
|
||||||
(MapFunction<Tuple2<Relation, Relation>, Relation>) s -> {
|
|
||||||
if (s._2() != null) {
|
|
||||||
s._1().setTarget(s._2().getSource());
|
|
||||||
}
|
|
||||||
return s._1();
|
|
||||||
},
|
|
||||||
Encoders.bean(Relation.class));
|
|
||||||
secondJoin.write().mode(SaveMode.Overwrite).save(targetPath + "_fixed");
|
|
||||||
|
|
||||||
FileSystem fileSystem = FileSystem.get(sc.hadoopConfiguration());
|
|
||||||
|
|
||||||
fileSystem.delete(new Path(targetPath), true);
|
|
||||||
fileSystem.rename(new Path(targetPath + "_fixed"), new Path(targetPath));
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
public static String getJPathString(final String jsonPath, final String json) {
|
|
||||||
try {
|
|
||||||
Object o = JsonPath.read(json, jsonPath);
|
|
||||||
if (o instanceof String)
|
|
||||||
return (String) o;
|
|
||||||
if (o instanceof JSONArray && ((JSONArray) o).size() > 0)
|
|
||||||
return (String) ((JSONArray) o).get(0);
|
|
||||||
return "";
|
|
||||||
} catch (Exception e) {
|
|
||||||
return "";
|
|
||||||
}
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,72 +0,0 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.sx.graph;
|
|
||||||
|
|
||||||
import org.apache.commons.io.IOUtils;
|
|
||||||
import org.apache.hadoop.io.IntWritable;
|
|
||||||
import org.apache.hadoop.io.Text;
|
|
||||||
import org.apache.hadoop.io.compress.GzipCodec;
|
|
||||||
import org.apache.spark.api.java.JavaSparkContext;
|
|
||||||
import org.apache.spark.api.java.function.FlatMapFunction;
|
|
||||||
import org.apache.spark.sql.SparkSession;
|
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
|
||||||
import eu.dnetlib.dhp.sx.graph.parser.DatasetScholexplorerParser;
|
|
||||||
import eu.dnetlib.dhp.sx.graph.parser.PublicationScholexplorerParser;
|
|
||||||
import eu.dnetlib.scholexplorer.relation.RelationMapper;
|
|
||||||
import scala.Tuple2;
|
|
||||||
|
|
||||||
/**
|
|
||||||
* This Job read a sequential File containing XML stored in the aggregator and generates an RDD of heterogeneous
|
|
||||||
* entities like Dataset, Relation, Publication and Unknown
|
|
||||||
*/
|
|
||||||
public class SparkScholexplorerGraphImporter {
|
|
||||||
|
|
||||||
public static void main(String[] args) throws Exception {
|
|
||||||
|
|
||||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
|
||||||
IOUtils
|
|
||||||
.toString(
|
|
||||||
SparkScholexplorerGraphImporter.class
|
|
||||||
.getResourceAsStream(
|
|
||||||
"/eu/dnetlib/dhp/sx/graph/argumentparser/input_graph_scholix_parameters.json")));
|
|
||||||
|
|
||||||
parser.parseArgument(args);
|
|
||||||
final SparkSession spark = SparkSession
|
|
||||||
.builder()
|
|
||||||
.appName(SparkScholexplorerGraphImporter.class.getSimpleName())
|
|
||||||
.master(parser.get("master"))
|
|
||||||
.getOrCreate();
|
|
||||||
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
|
|
||||||
final String inputPath = parser.get("sourcePath");
|
|
||||||
|
|
||||||
RelationMapper relationMapper = RelationMapper.load();
|
|
||||||
|
|
||||||
sc
|
|
||||||
.sequenceFile(inputPath, IntWritable.class, Text.class)
|
|
||||||
.map(Tuple2::_2)
|
|
||||||
.map(Text::toString)
|
|
||||||
.repartition(500)
|
|
||||||
.flatMap(
|
|
||||||
(FlatMapFunction<String, Oaf>) record -> {
|
|
||||||
switch (parser.get("entity")) {
|
|
||||||
case "dataset":
|
|
||||||
final DatasetScholexplorerParser d = new DatasetScholexplorerParser();
|
|
||||||
return d.parseObject(record, relationMapper).iterator();
|
|
||||||
case "publication":
|
|
||||||
final PublicationScholexplorerParser p = new PublicationScholexplorerParser();
|
|
||||||
return p.parseObject(record, relationMapper).iterator();
|
|
||||||
default:
|
|
||||||
throw new IllegalArgumentException("wrong values of entities");
|
|
||||||
}
|
|
||||||
})
|
|
||||||
.map(
|
|
||||||
k -> {
|
|
||||||
ObjectMapper mapper = new ObjectMapper();
|
|
||||||
return mapper.writeValueAsString(k);
|
|
||||||
})
|
|
||||||
.saveAsTextFile(parser.get("targetPath"), GzipCodec.class);
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
@ -1,203 +0,0 @@
|
||||||
package eu.dnetlib.dhp.sx.graph
|
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result}
|
|
||||||
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication, DLIUnknown}
|
|
||||||
import eu.dnetlib.dhp.sx.graph.ebi.EBIAggregator
|
|
||||||
import org.apache.commons.io.IOUtils
|
|
||||||
import org.apache.commons.lang3.StringUtils
|
|
||||||
import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession}
|
|
||||||
import org.slf4j.LoggerFactory
|
|
||||||
import org.apache.spark.sql.functions.col
|
|
||||||
|
|
||||||
|
|
||||||
object SparkSplitOafTODLIEntities {
|
|
||||||
|
|
||||||
|
|
||||||
def getKeyRelation(rel:Relation):String = {
|
|
||||||
s"${rel.getSource}::${rel.getRelType}::${rel.getTarget}"
|
|
||||||
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
def extract_dataset(spark:SparkSession, workingPath:String) :Unit = {
|
|
||||||
|
|
||||||
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
|
|
||||||
implicit val datEncoder: Encoder[DLIDataset] = Encoders.kryo[DLIDataset]
|
|
||||||
|
|
||||||
val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf].repartition(4000)
|
|
||||||
|
|
||||||
val ebi_dataset:Dataset[DLIDataset] = spark.read.load(s"$workingPath/ebi/baseline_dataset_ebi").as[DLIDataset].repartition(1000)
|
|
||||||
|
|
||||||
|
|
||||||
OAFDataset
|
|
||||||
.filter(s => s != null && s.isInstanceOf[DLIDataset])
|
|
||||||
.map(s =>s.asInstanceOf[DLIDataset])
|
|
||||||
.union(ebi_dataset)
|
|
||||||
.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, datEncoder))
|
|
||||||
.groupByKey(_._1)(Encoders.STRING)
|
|
||||||
.agg(EBIAggregator.getDLIDatasetAggregator().toColumn)
|
|
||||||
.map(p => p._2)
|
|
||||||
.repartition(2000)
|
|
||||||
.write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/dataset")
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
def extract_publication(spark:SparkSession, workingPath:String) :Unit = {
|
|
||||||
|
|
||||||
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
|
|
||||||
implicit val pubEncoder: Encoder[DLIPublication] = Encoders.kryo[DLIPublication]
|
|
||||||
|
|
||||||
val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf]
|
|
||||||
|
|
||||||
val ebi_publication:Dataset[DLIPublication] = spark.read.load(s"$workingPath/ebi/baseline_publication_ebi").as[DLIPublication].repartition(1000)
|
|
||||||
|
|
||||||
|
|
||||||
OAFDataset
|
|
||||||
.filter(s => s != null && s.isInstanceOf[DLIPublication])
|
|
||||||
.map(s =>s.asInstanceOf[DLIPublication])
|
|
||||||
.union(ebi_publication)
|
|
||||||
.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, pubEncoder))
|
|
||||||
.groupByKey(_._1)(Encoders.STRING)
|
|
||||||
.agg(EBIAggregator.getDLIPublicationAggregator().toColumn)
|
|
||||||
.map(p => p._2)
|
|
||||||
.repartition(2000)
|
|
||||||
.write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/publication")
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
def extract_unknown(spark:SparkSession, workingPath:String) :Unit = {
|
|
||||||
|
|
||||||
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
|
|
||||||
implicit val unkEncoder: Encoder[DLIUnknown] = Encoders.kryo[DLIUnknown]
|
|
||||||
|
|
||||||
val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf]
|
|
||||||
|
|
||||||
OAFDataset
|
|
||||||
.filter(s => s != null && s.isInstanceOf[DLIUnknown])
|
|
||||||
.map(s =>s.asInstanceOf[DLIUnknown])
|
|
||||||
.map(d => (d.getId, d))(Encoders.tuple(Encoders.STRING, unkEncoder))
|
|
||||||
.groupByKey(_._1)(Encoders.STRING)
|
|
||||||
.agg(EBIAggregator.getDLIUnknownAggregator().toColumn)
|
|
||||||
.map(p => p._2)
|
|
||||||
.write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/unknown")
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
def extract_ids(o:Oaf) :(String, String) = {
|
|
||||||
|
|
||||||
o match {
|
|
||||||
case p: DLIPublication =>
|
|
||||||
val prefix = StringUtils.substringBefore(p.getId, "|")
|
|
||||||
val original = StringUtils.substringAfter(p.getOriginalObjIdentifier, "::")
|
|
||||||
(p.getId, s"$prefix|$original")
|
|
||||||
case p: DLIDataset =>
|
|
||||||
val prefix = StringUtils.substringBefore(p.getId, "|")
|
|
||||||
val original = StringUtils.substringAfter(p.getOriginalObjIdentifier, "::")
|
|
||||||
(p.getId, s"$prefix|$original")
|
|
||||||
case _ =>null
|
|
||||||
}
|
|
||||||
}
|
|
||||||
|
|
||||||
def extract_relations(spark:SparkSession, workingPath:String) :Unit = {
|
|
||||||
|
|
||||||
implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf]
|
|
||||||
implicit val relEncoder: Encoder[Relation] = Encoders.kryo[Relation]
|
|
||||||
import spark.implicits._
|
|
||||||
|
|
||||||
val OAFDataset:Dataset[Oaf] = spark.read.load(s"$workingPath/input/OAFDataset").as[Oaf]
|
|
||||||
val ebi_relation:Dataset[Relation] = spark.read.load(s"$workingPath/ebi/baseline_relation_ebi").as[Relation].repartition(2000)
|
|
||||||
|
|
||||||
|
|
||||||
OAFDataset
|
|
||||||
.filter(o => o.isInstanceOf[Result])
|
|
||||||
.map(extract_ids)(Encoders.tuple(Encoders.STRING, Encoders.STRING))
|
|
||||||
.filter(r => r != null)
|
|
||||||
.where("_1 != _2")
|
|
||||||
.select(col("_1").alias("newId"), col("_2").alias("oldId"))
|
|
||||||
.distinct()
|
|
||||||
.map(f => IdReplace(f.getString(0), f.getString(1)))
|
|
||||||
.write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/id_replace")
|
|
||||||
|
|
||||||
|
|
||||||
OAFDataset
|
|
||||||
.filter(s => s != null && s.isInstanceOf[Relation])
|
|
||||||
.map(s =>s.asInstanceOf[Relation])
|
|
||||||
.union(ebi_relation)
|
|
||||||
.map(d => (getKeyRelation(d), d))(Encoders.tuple(Encoders.STRING, relEncoder))
|
|
||||||
.groupByKey(_._1)(Encoders.STRING)
|
|
||||||
.agg(EBIAggregator.getRelationAggregator().toColumn)
|
|
||||||
.map(p => p._2)
|
|
||||||
.repartition(4000)
|
|
||||||
.write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/relation_unfixed")
|
|
||||||
|
|
||||||
|
|
||||||
val relations = spark.read.load(s"$workingPath/graph/relation_unfixed").as[Relation]
|
|
||||||
val ids = spark.read.load(s"$workingPath/graph/id_replace").as[IdReplace]
|
|
||||||
|
|
||||||
relations
|
|
||||||
.map(r => (r.getSource, r))(Encoders.tuple(Encoders.STRING, relEncoder))
|
|
||||||
.joinWith(ids, col("_1").equalTo(ids("oldId")), "left")
|
|
||||||
.map(i =>{
|
|
||||||
val r = i._1._2
|
|
||||||
if (i._2 != null)
|
|
||||||
{
|
|
||||||
val id = i._2.newId
|
|
||||||
r.setSource(id)
|
|
||||||
}
|
|
||||||
r
|
|
||||||
}).write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/rel_f_source")
|
|
||||||
|
|
||||||
val rel_source:Dataset[Relation] = spark.read.load(s"$workingPath/graph/rel_f_source").as[Relation]
|
|
||||||
|
|
||||||
rel_source
|
|
||||||
.map(r => (r.getTarget, r))(Encoders.tuple(Encoders.STRING, relEncoder))
|
|
||||||
.joinWith(ids, col("_1").equalTo(ids("oldId")), "left")
|
|
||||||
.map(i =>{
|
|
||||||
val r:Relation = i._1._2
|
|
||||||
if (i._2 != null)
|
|
||||||
{
|
|
||||||
val id = i._2.newId
|
|
||||||
r.setTarget(id)
|
|
||||||
}
|
|
||||||
r
|
|
||||||
}).write.mode(SaveMode.Overwrite).save(s"$workingPath/graph/relation")
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
|
||||||
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkSplitOafTODLIEntities.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/argumentparser/input_extract_entities_parameters.json")))
|
|
||||||
val logger = LoggerFactory.getLogger(SparkSplitOafTODLIEntities.getClass)
|
|
||||||
parser.parseArgument(args)
|
|
||||||
|
|
||||||
val workingPath: String = parser.get("workingPath")
|
|
||||||
val entity:String = parser.get("entity")
|
|
||||||
logger.info(s"Working dir path = $workingPath")
|
|
||||||
|
|
||||||
val spark:SparkSession = SparkSession
|
|
||||||
.builder()
|
|
||||||
.appName(SparkSplitOafTODLIEntities.getClass.getSimpleName)
|
|
||||||
.config("spark.serializer", "org.apache.spark.serializer.KryoSerializer")
|
|
||||||
.master(parser.get("master"))
|
|
||||||
.getOrCreate()
|
|
||||||
|
|
||||||
|
|
||||||
entity match {
|
|
||||||
case "publication" => extract_publication(spark, workingPath)
|
|
||||||
case "dataset" => extract_dataset(spark,workingPath)
|
|
||||||
case "relation" => extract_relations(spark, workingPath)
|
|
||||||
case "unknown" => extract_unknown(spark, workingPath)
|
|
||||||
}
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
@ -1,73 +0,0 @@
|
||||||
package eu.dnetlib.dhp.sx.graph
|
|
||||||
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation}
|
|
||||||
import eu.dnetlib.dhp.schema.scholexplorer.{DLIDataset, DLIPublication}
|
|
||||||
import eu.dnetlib.dhp.sx.graph.parser.{DatasetScholexplorerParser, PublicationScholexplorerParser}
|
|
||||||
import eu.dnetlib.scholexplorer.relation.RelationMapper
|
|
||||||
import org.apache.commons.io.IOUtils
|
|
||||||
import org.apache.hadoop.io.{IntWritable, Text}
|
|
||||||
import org.apache.spark.SparkConf
|
|
||||||
import org.apache.spark.rdd.RDD
|
|
||||||
import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession}
|
|
||||||
import org.slf4j.LoggerFactory
|
|
||||||
|
|
||||||
import scala.collection.JavaConverters._
|
|
||||||
|
|
||||||
|
|
||||||
/**
|
|
||||||
* This new version of the Job read a sequential File containing XML stored in the aggregator and generates a Dataset OAF of heterogeneous
|
|
||||||
* entities like Dataset, Relation, Publication and Unknown
|
|
||||||
*/
|
|
||||||
|
|
||||||
object SparkXMLToOAFDataset {
|
|
||||||
|
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
|
||||||
val logger = LoggerFactory.getLogger(SparkXMLToOAFDataset.getClass)
|
|
||||||
val conf = new SparkConf()
|
|
||||||
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkXMLToOAFDataset.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/argumentparser/input_graph_scholix_parameters.json")))
|
|
||||||
parser.parseArgument(args)
|
|
||||||
val spark =
|
|
||||||
SparkSession
|
|
||||||
.builder()
|
|
||||||
.config(conf)
|
|
||||||
.appName(SparkXMLToOAFDataset.getClass.getSimpleName)
|
|
||||||
.master(parser.get("master")).getOrCreate()
|
|
||||||
|
|
||||||
val sc = spark.sparkContext
|
|
||||||
|
|
||||||
implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf]
|
|
||||||
implicit val datasetEncoder:Encoder[DLIDataset] = Encoders.kryo[DLIDataset]
|
|
||||||
implicit val publicationEncoder:Encoder[DLIPublication] = Encoders.kryo[DLIPublication]
|
|
||||||
implicit val relationEncoder:Encoder[Relation] = Encoders.kryo[Relation]
|
|
||||||
|
|
||||||
val relationMapper = RelationMapper.load
|
|
||||||
|
|
||||||
val inputPath: String = parser.get("sourcePath")
|
|
||||||
val entity: String = parser.get("entity")
|
|
||||||
val targetPath = parser.get("targetPath")
|
|
||||||
|
|
||||||
logger.info(s"Input path is $inputPath")
|
|
||||||
logger.info(s"Entity path is $entity")
|
|
||||||
logger.info(s"Target Path is $targetPath")
|
|
||||||
|
|
||||||
val scholixRdd:RDD[Oaf] = sc.sequenceFile(inputPath, classOf[IntWritable], classOf[Text])
|
|
||||||
.map(s => s._2.toString)
|
|
||||||
.flatMap(s => {
|
|
||||||
entity match {
|
|
||||||
case "publication" =>
|
|
||||||
val p = new PublicationScholexplorerParser
|
|
||||||
val l =p.parseObject(s, relationMapper)
|
|
||||||
if (l != null) l.asScala else List()
|
|
||||||
case "dataset" =>
|
|
||||||
val d = new DatasetScholexplorerParser
|
|
||||||
val l =d.parseObject(s, relationMapper)
|
|
||||||
if (l != null) l.asScala else List()
|
|
||||||
}
|
|
||||||
}).filter(s => s!= null)
|
|
||||||
spark.createDataset(scholixRdd).write.mode(SaveMode.Append).save(targetPath)
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
||||||
}
|
|
||||||
|
|
@ -11,9 +11,9 @@ import org.slf4j.{Logger, LoggerFactory}
|
||||||
object SparkEBILinksToOaf {
|
object SparkEBILinksToOaf {
|
||||||
|
|
||||||
def main(args: Array[String]): Unit = {
|
def main(args: Array[String]): Unit = {
|
||||||
val log: Logger = LoggerFactory.getLogger(SparkEBILinksToOaf.getClass)
|
val log: Logger = LoggerFactory.getLogger(getClass)
|
||||||
val conf: SparkConf = new SparkConf()
|
val conf: SparkConf = new SparkConf()
|
||||||
val parser = new ArgumentApplicationParser(IOUtils.toString(SparkEBILinksToOaf.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/ebi/ebi_to_df_params.json")))
|
val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/ebi/ebi_to_df_params.json")))
|
||||||
parser.parseArgument(args)
|
parser.parseArgument(args)
|
||||||
val spark: SparkSession =
|
val spark: SparkSession =
|
||||||
SparkSession
|
SparkSession
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,5 @@
|
||||||
|
[
|
||||||
|
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||||
|
{"paramName":"s", "paramLongName":"sourcePath", "paramDescription": "the source Path", "paramRequired": true},
|
||||||
|
{"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the path of the raw graph", "paramRequired": true}
|
||||||
|
]
|
||||||
|
|
@ -0,0 +1,6 @@
|
||||||
|
[
|
||||||
|
{"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true},
|
||||||
|
{"paramName":"r", "paramLongName":"relationPath", "paramDescription": "the source Path", "paramRequired": true},
|
||||||
|
{"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the source Path", "paramRequired": true},
|
||||||
|
{"paramName":"e", "paramLongName":"entityPath", "paramDescription": "the path of the raw graph", "paramRequired": true}
|
||||||
|
]
|
||||||
|
|
@ -1,121 +1,72 @@
|
||||||
<workflow-app name="Create Raw Graph Step 1: import Entities from aggregator to HDFS" xmlns="uri:oozie:workflow:0.5">
|
<workflow-app name="Create Raw Graph Step 1: extract Entities in raw graph" xmlns="uri:oozie:workflow:0.5">
|
||||||
<parameters>
|
<parameters>
|
||||||
<property>
|
<property>
|
||||||
<name>reuseContent</name>
|
<name>sourcePath</name>
|
||||||
<value>false</value>
|
|
||||||
<description>should import content from the aggregator or reuse a previous version</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>workingPath</name>
|
|
||||||
<description>the working dir base path</description>
|
<description>the working dir base path</description>
|
||||||
</property>
|
</property>
|
||||||
<property>
|
<property>
|
||||||
<name>targetXMLPath</name>
|
<name>targetPath</name>
|
||||||
<description>the graph Raw base path</description>
|
<description>the graph Raw base path</description>
|
||||||
</property>
|
</property>
|
||||||
<property>
|
|
||||||
<name>targetEntityPath</name>
|
|
||||||
<description>the graph Raw base path</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>format</name>
|
|
||||||
<description>the postgres URL to access to the database</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>layout</name>
|
|
||||||
<description>the user postgres</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>interpretation</name>
|
|
||||||
<description>the password postgres</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>dbhost</name>
|
|
||||||
<description>mongoDB url, example: mongodb://[username:password@]host[:port]</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>dbName</name>
|
|
||||||
<description>mongo database</description>
|
|
||||||
</property>
|
|
||||||
<property>
|
|
||||||
<name>entity</name>
|
|
||||||
<description>the entity type</description>
|
|
||||||
</property>
|
|
||||||
</parameters>
|
</parameters>
|
||||||
|
|
||||||
<start to="ReuseContent"/>
|
<start to="ResolveRelations"/>
|
||||||
|
|
||||||
<decision name="ReuseContent">
|
|
||||||
<switch>
|
|
||||||
<case to="ImportEntitiesFromMongo">${wf:conf('reuseContent') eq false}</case>
|
|
||||||
<case to="ConvertXML2Entity">${wf:conf('reuseContent') eq true}</case>
|
|
||||||
<default to="ResetWorkingPath"/>
|
|
||||||
</switch>
|
|
||||||
</decision>
|
|
||||||
|
|
||||||
|
|
||||||
<kill name="Kill">
|
<kill name="Kill">
|
||||||
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
|
||||||
</kill>
|
</kill>
|
||||||
|
|
||||||
<action name="ResetWorkingPath">
|
<action name="ExtractEntities">
|
||||||
<fs>
|
|
||||||
<delete path='${workingPath}'/>
|
|
||||||
<mkdir path='${workingPath}/input'/>
|
|
||||||
</fs>
|
|
||||||
<ok to="ImportEntitiesFromMongo"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
|
|
||||||
<action name="ImportEntitiesFromMongo">
|
|
||||||
<java>
|
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<main-class>eu.dnetlib.dhp.sx.graph.ImportDataFromMongo</main-class>
|
|
||||||
<arg>-t</arg><arg>${targetXMLPath}</arg>
|
|
||||||
<arg>-n</arg><arg>${nameNode}</arg>
|
|
||||||
<arg>-h</arg><arg>${dbhost}</arg>
|
|
||||||
<arg>-p</arg><arg>27017</arg>
|
|
||||||
<arg>-dn</arg><arg>${dbName}</arg>
|
|
||||||
<arg>-f</arg><arg>${format}</arg>
|
|
||||||
<arg>-l</arg><arg>${layout}</arg>
|
|
||||||
<arg>-i</arg><arg>${interpretation}</arg>
|
|
||||||
</java>
|
|
||||||
<ok to="ResetTargetPath"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="ResetTargetPath">
|
|
||||||
<fs>
|
|
||||||
<delete path='${targetEntityPath}'/>
|
|
||||||
</fs>
|
|
||||||
<ok to="ConvertXML2Entity"/>
|
|
||||||
<error to="Kill"/>
|
|
||||||
</action>
|
|
||||||
|
|
||||||
<action name="ConvertXML2Entity">
|
|
||||||
<spark xmlns="uri:oozie:spark-action:0.2">
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
<job-tracker>${jobTracker}</job-tracker>
|
<master>yarn</master>
|
||||||
<name-node>${nameNode}</name-node>
|
|
||||||
<master>yarn-cluster</master>
|
|
||||||
<mode>cluster</mode>
|
<mode>cluster</mode>
|
||||||
<name>Import ${entity} and related entities</name>
|
<name>Extract entities in raw graph</name>
|
||||||
<class>eu.dnetlib.dhp.sx.graph.SparkXMLToOAFDataset</class>
|
<class>eu.dnetlib.dhp.sx.graph.SparkCreateInputGraph</class>
|
||||||
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
<spark-opts>
|
<spark-opts>
|
||||||
--executor-memory ${sparkExecutorMemory}
|
--executor-memory=${sparkExecutorMemory}
|
||||||
--executor-cores=${sparkExecutorCores}
|
--executor-cores=${sparkExecutorCores}
|
||||||
--driver-memory=${sparkDriverMemory}
|
--driver-memory=${sparkDriverMemory}
|
||||||
${sparkExtraOPT}
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.shuffle.partitions=2000
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
</spark-opts>
|
</spark-opts>
|
||||||
<arg>-mt</arg> <arg>yarn</arg>
|
<arg>--master</arg><arg>yarn</arg>
|
||||||
<arg>--sourcePath</arg><arg>${targetXMLPath}</arg>
|
<arg>--sourcePath</arg><arg>${sourcePath}</arg>
|
||||||
<arg>--targetPath</arg><arg>${workingPath}/input/OAFDataset</arg>
|
<arg>--targetPath</arg><arg>${targetPath}</arg>
|
||||||
<arg>--entity</arg><arg>${entity}</arg>
|
</spark>
|
||||||
|
<ok to="ResolveRelations"/>
|
||||||
|
<error to="Kill"/>
|
||||||
|
</action>
|
||||||
|
|
||||||
|
|
||||||
|
<action name="ResolveRelations">
|
||||||
|
<spark xmlns="uri:oozie:spark-action:0.2">
|
||||||
|
<master>yarn</master>
|
||||||
|
<mode>cluster</mode>
|
||||||
|
<name>Resolve Relations in raw graph</name>
|
||||||
|
<class>eu.dnetlib.dhp.sx.graph.SparkResolveRelation</class>
|
||||||
|
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
|
||||||
|
<spark-opts>
|
||||||
|
--executor-memory=${sparkExecutorMemory}
|
||||||
|
--executor-cores=${sparkExecutorCores}
|
||||||
|
--driver-memory=${sparkDriverMemory}
|
||||||
|
--conf spark.extraListeners=${spark2ExtraListeners}
|
||||||
|
--conf spark.sql.shuffle.partitions=3000
|
||||||
|
--conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners}
|
||||||
|
--conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress}
|
||||||
|
--conf spark.eventLog.dir=${nameNode}${spark2EventLogDir}
|
||||||
|
</spark-opts>
|
||||||
|
<arg>--master</arg><arg>yarn</arg>
|
||||||
|
<arg>--relationPath</arg><arg>${targetPath}/extracted/relation</arg>
|
||||||
|
<arg>--workingPath</arg><arg>${targetPath}/resolved/</arg>
|
||||||
|
<arg>--entityPath</arg><arg>${targetPath}/dedup</arg>
|
||||||
</spark>
|
</spark>
|
||||||
<ok to="End"/>
|
<ok to="End"/>
|
||||||
<error to="Kill"/>
|
<error to="Kill"/>
|
||||||
</action>
|
</action>
|
||||||
|
|
||||||
<end name="End"/>
|
<end name="End"/>
|
||||||
</workflow-app>
|
</workflow-app>
|
||||||
Loading…
Reference in New Issue