package eu.dnetlib.dhp.oa.graph.merge; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.*; import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.function.FilterFunction; import org.apache.spark.api.java.function.MapFunction; 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 org.slf4j.Logger; import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.HdfsSupport; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.*; import scala.Tuple2; /** * Combines the content from two aggregator graph tables of the same type, entities (or relationships) with the same ids * are picked preferring those from the BETA aggregator rather then from PROD. The identity of a relationship is defined * by eu.dnetlib.dhp.schema.common.ModelSupport#idFn() */ public class MergeGraphTableSparkJob { private static final Logger log = LoggerFactory.getLogger(MergeGraphTableSparkJob.class); private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private static final String PRIORITY_DEFAULT = "BETA"; // BETA | PROD private static final Datasource DATASOURCE = new Datasource(); static { Qualifier compatibility = new Qualifier(); compatibility.setClassid(ModelConstants.UNKNOWN); DATASOURCE.setOpenairecompatibility(compatibility); } public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils .toString( Objects .requireNonNull( MergeGraphTableSparkJob.class .getResourceAsStream( "/eu/dnetlib/dhp/oa/graph/merge_graphs_parameters.json"))); final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); parser.parseArgument(args); String priority = Optional .ofNullable(parser.get("priority")) .orElse(PRIORITY_DEFAULT); log.info("priority: {}", priority); Boolean isSparkSessionManaged = Optional .ofNullable(parser.get("isSparkSessionManaged")) .map(Boolean::valueOf) .orElse(Boolean.TRUE); log.info("isSparkSessionManaged: {}", isSparkSessionManaged); String betaInputPath = parser.get("betaInputPath"); log.info("betaInputPath: {}", betaInputPath); String prodInputPath = parser.get("prodInputPath"); log.info("prodInputPath: {}", prodInputPath); String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); String graphTableClassName = parser.get("graphTableClassName"); log.info("graphTableClassName: {}", graphTableClassName); Class entityClazz = (Class) Class.forName(graphTableClassName); SparkConf conf = new SparkConf(); conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer"); conf.registerKryoClasses(ModelSupport.getOafModelClasses()); runWithSparkSession( conf, isSparkSessionManaged, spark -> { removeOutputDir(spark, outputPath); mergeGraphTable(spark, priority, betaInputPath, prodInputPath, entityClazz, entityClazz, outputPath); }); } private static

void mergeGraphTable( SparkSession spark, String priority, String betaInputPath, String prodInputPath, Class

p_clazz, Class b_clazz, String outputPath) { Dataset> beta = readTableFromPath(spark, betaInputPath, b_clazz); Dataset> prod = readTableFromPath(spark, prodInputPath, p_clazz); prod .joinWith(beta, prod.col("_1").equalTo(beta.col("_1")), "full_outer") .map((MapFunction, Tuple2>, P>) value -> { Optional

p = Optional.ofNullable(value._1()).map(Tuple2::_2); Optional b = Optional.ofNullable(value._2()).map(Tuple2::_2); if (p.orElse((P) b.orElse((B) DATASOURCE)) instanceof Datasource) { return mergeDatasource(p, b); } switch (priority) { default: case "BETA": return mergeWithPriorityToBETA(p, b); case "PROD": return mergeWithPriorityToPROD(p, b); } }, Encoders.bean(p_clazz)) .filter((FilterFunction

) Objects::nonNull) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(outputPath); } /** * Datasources involved in the merge operation doesn't obey to the infra precedence policy, but relies on a custom * behaviour that, given two datasources from beta and prod returns the one from prod with the highest * compatibility among the two. * * @param p datasource from PROD * @param b datasource from BETA * @param

Datasource class type from PROD * @param Datasource class type from BETA * @return the datasource from PROD with the highest compatibility level. */ protected static

P mergeDatasource(Optional

p, Optional b) { if (p.isPresent() & !b.isPresent()) { return p.get(); } if (b.isPresent() & !p.isPresent()) { return (P) b.get(); } if (!b.isPresent() & !p.isPresent()) { return null; // unlikely, at least one should be produced by the join operation } Datasource dp = (Datasource) p.get(); Datasource db = (Datasource) b.get(); List list = Arrays.asList(dp.getOpenairecompatibility(), db.getOpenairecompatibility()); dp.setOpenairecompatibility(Collections.min(list, new DatasourceCompatibilityComparator())); return (P) dp; } private static

P mergeWithPriorityToPROD(Optional

p, Optional b) { if (b.isPresent() & !p.isPresent()) { return (P) b.get(); } if (p.isPresent()) { return p.get(); } return null; } private static

P mergeWithPriorityToBETA(Optional

p, Optional b) { if (p.isPresent() & !b.isPresent()) { return p.get(); } if (b.isPresent()) { return (P) b.get(); } return null; } private static Dataset> readTableFromPath( SparkSession spark, String inputEntityPath, Class clazz) { log.info("Reading Graph table from: {}", inputEntityPath); return spark .read() .textFile(inputEntityPath) .map( (MapFunction>) value -> { final T t = OBJECT_MAPPER.readValue(value, clazz); final String id = ModelSupport.idFn().apply(t); return new Tuple2<>(id, t); }, Encoders.tuple(Encoders.STRING(), Encoders.kryo(clazz))); } private static void removeOutputDir(SparkSession spark, String path) { HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); } }