package eu.dnetlib.dedup; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.pace.config.DedupConfig; import eu.dnetlib.pace.model.MapDocument; import eu.dnetlib.pace.util.MapDocumentUtil; import org.apache.commons.io.IOUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.hadoop.io.Text; import org.apache.hadoop.io.compress.GzipCodec; import org.apache.hadoop.mapred.SequenceFileOutputFormat; import org.apache.spark.SparkConf; 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.sql.Encoders; import org.apache.spark.sql.SparkSession; import scala.Tuple2; import eu.dnetlib.actionmanager.actions.AtomicAction; import eu.dnetlib.actionmanager.common.Agent; import java.io.Serializable; import java.util.Arrays; import java.util.List; import java.util.stream.Collectors; public class SparkCreateSimRels2 implements Serializable { final static String CONF_SEPARATOR = "@@@"; private static final Log log = LogFactory.getLog(SparkCreateSimRels2.class); public static List decompressConfs(String compressedConfs){ return Arrays.stream(compressedConfs.split(CONF_SEPARATOR)) .map(ArgumentApplicationParser::decompressValue) .map(DedupConfig::load) .collect(Collectors.toList()); } public static void main(String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCreateSimRels.class.getResourceAsStream("/eu/dnetlib/dhp/dedup/dedup_parameters.json"))); parser.parseArgument(args); new SparkCreateSimRels2().run(parser, decompressConfs(parser.get("dedupConf"))); } private void run(ArgumentApplicationParser parser, List dedupConfs) { //read oozie parameters final String sourcePath = parser.get("sourcePath"); final String targetPath = parser.get("targetPath"); final String rawSetName = parser.get("rawSet"); final String agentId = parser.get("agentId"); final String agentName = parser.get("agentName"); try (SparkSession spark = getSparkSession(parser)) { final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); //create empty sequenceFile for the accumulation JavaRDD> simRel = sc.emptyRDD(); //for each dedup configuration for (DedupConfig dedupConf: dedupConfs) { final String entity = dedupConf.getWf().getEntityType(); JavaPairRDD mapDocument = sc.textFile(sourcePath + "/" + entity) .mapToPair(s -> { MapDocument d = MapDocumentUtil.asMapDocumentWithJPath(dedupConf, s); return new Tuple2<>(d.getIdentifier(), d); }); //create blocks for deduplication JavaPairRDD> blocks = Deduper.createsortedBlocks(sc, mapDocument, dedupConf); //create relations by comparing only elements in the same group final JavaPairRDD dedupRels = Deduper.computeRelations2(sc, blocks, dedupConf); JavaRDD relationsRDD = dedupRels.map(r -> createSimRel(r._1(), r._2())); //create atomic actions JavaRDD> newSimRels = relationsRDD .mapToPair(rel -> new Tuple2<>( createActionId(rel.getSource(), rel.getTarget(), entity), //TODO update the type, maybe take it from the configuration? new AtomicAction(rawSetName, new Agent(agentId, agentName, Agent.AGENT_TYPE.service), rel.getSource(), "isSimilarTo", rel.getTarget(), new ObjectMapper().writeValueAsString(rel).getBytes()))) .map(aa -> new Tuple2<>(aa._1(), transformAction(aa._2()))); simRel = simRel.union(newSimRels); } String targetDirectory = targetPath + "/" + rawSetName; // simRel.map(s -> s._1().toString()).saveAsTextFile(targetDirectory); simRel.mapToPair(r -> r) .saveAsHadoopFile(targetDirectory, Text.class, Text.class, SequenceFileOutputFormat.class, GzipCodec.class); } } public Text createActionId(String source, String target, String type) { String id = source + "@" + type + "@" + target; return new Text(id); } public Text transformAction(AtomicAction aa) throws JsonProcessingException { ObjectMapper mapper = new ObjectMapper(); return new Text(mapper.writeValueAsString(aa)); } public Relation createSimRel(String source, String target){ final Relation r = new Relation(); r.setSource(source); r.setTarget(target); r.setRelClass("isSimilarTo"); return r; } private static SparkSession getSparkSession(ArgumentApplicationParser parser) { SparkConf conf = new SparkConf(); return SparkSession .builder() .appName(SparkCreateSimRels2.class.getSimpleName()) .master(parser.get("master")) .config(conf) // .enableHiveSupport() .getOrCreate(); } }