179 lines
6.0 KiB
Java
179 lines
6.0 KiB
Java
|
|
package eu.dnetlib.dhp.oa.dedup;
|
|
|
|
import java.io.IOException;
|
|
import java.util.Map;
|
|
|
|
import org.apache.commons.io.IOUtils;
|
|
import org.apache.hadoop.conf.Configuration;
|
|
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.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.Dataset;
|
|
import org.apache.spark.sql.Encoders;
|
|
import org.apache.spark.sql.Row;
|
|
import org.apache.spark.sql.SparkSession;
|
|
import org.slf4j.Logger;
|
|
import org.slf4j.LoggerFactory;
|
|
|
|
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
import eu.dnetlib.dhp.common.HdfsSupport;
|
|
import eu.dnetlib.dhp.schema.common.EntityType;
|
|
import eu.dnetlib.dhp.schema.common.ModelSupport;
|
|
import eu.dnetlib.dhp.schema.oaf.DataInfo;
|
|
import eu.dnetlib.dhp.schema.oaf.Oaf;
|
|
import eu.dnetlib.dhp.schema.oaf.OafEntity;
|
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
import eu.dnetlib.dhp.utils.ISLookupClientFactory;
|
|
import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService;
|
|
import eu.dnetlib.pace.util.MapDocumentUtil;
|
|
import scala.Tuple2;
|
|
|
|
public class SparkUpdateEntity extends AbstractSparkAction {
|
|
|
|
private static final Logger log = LoggerFactory.getLogger(SparkUpdateEntity.class);
|
|
|
|
private static final String IDJSONPATH = "$.id";
|
|
|
|
public SparkUpdateEntity(ArgumentApplicationParser parser, SparkSession spark) {
|
|
super(parser, spark);
|
|
}
|
|
|
|
public static void main(String[] args) throws Exception {
|
|
ArgumentApplicationParser parser = new ArgumentApplicationParser(
|
|
IOUtils
|
|
.toString(
|
|
SparkUpdateEntity.class
|
|
.getResourceAsStream(
|
|
"/eu/dnetlib/dhp/oa/dedup/updateEntity_parameters.json")));
|
|
parser.parseArgument(args);
|
|
|
|
SparkConf conf = new SparkConf();
|
|
conf.set("spark.serializer", "org.apache.spark.serializer.KryoSerializer");
|
|
conf.registerKryoClasses(ModelSupport.getOafModelClasses());
|
|
|
|
new SparkUpdateEntity(parser, getSparkSession(conf))
|
|
.run(ISLookupClientFactory.getLookUpService(parser.get("isLookUpUrl")));
|
|
}
|
|
|
|
public void run(ISLookUpService isLookUpService) throws IOException {
|
|
|
|
final String graphBasePath = parser.get("graphBasePath");
|
|
final String workingPath = parser.get("workingPath");
|
|
final String dedupGraphPath = parser.get("dedupGraphPath");
|
|
|
|
log.info("graphBasePath: '{}'", graphBasePath);
|
|
log.info("workingPath: '{}'", workingPath);
|
|
log.info("dedupGraphPath: '{}'", dedupGraphPath);
|
|
|
|
final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
|
|
|
|
for (Map.Entry<EntityType, Class> e : ModelSupport.entityTypes.entrySet()) {
|
|
final EntityType type = e.getKey();
|
|
final Class clazz = e.getValue();
|
|
final String outputPath = dedupGraphPath + "/" + type;
|
|
removeOutputDir(spark, outputPath);
|
|
final String ip = DedupUtility.createEntityPath(graphBasePath, type.toString());
|
|
if (HdfsSupport.exists(ip, sc.hadoopConfiguration())) {
|
|
JavaRDD<String> sourceEntity = sc
|
|
.textFile(DedupUtility.createEntityPath(graphBasePath, type.toString()));
|
|
|
|
if (mergeRelExists(workingPath, type.toString())) {
|
|
|
|
final String mergeRelPath = DedupUtility
|
|
.createMergeRelPath(workingPath, "*", type.toString());
|
|
final String dedupRecordPath = DedupUtility
|
|
.createDedupRecordPath(workingPath, "*", type.toString());
|
|
|
|
final Dataset<Relation> rel = spark
|
|
.read()
|
|
.load(mergeRelPath)
|
|
.as(Encoders.bean(Relation.class));
|
|
|
|
final JavaPairRDD<String, String> mergedIds = rel
|
|
.where("relClass == 'merges'")
|
|
.where("source != target")
|
|
.select(rel.col("target"))
|
|
.distinct()
|
|
.toJavaRDD()
|
|
.mapToPair(
|
|
(PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(0), "d"));
|
|
|
|
JavaPairRDD<String, String> entitiesWithId = sourceEntity
|
|
.mapToPair(
|
|
(PairFunction<String, String, String>) s -> new Tuple2<>(
|
|
MapDocumentUtil.getJPathString(IDJSONPATH, s), s));
|
|
if (type == EntityType.organization) // exclude root records from organizations
|
|
entitiesWithId = excludeRootOrgs(entitiesWithId, rel);
|
|
|
|
JavaRDD<String> map = entitiesWithId
|
|
.leftOuterJoin(mergedIds)
|
|
.map(k -> {
|
|
if (k._2()._2().isPresent()) {
|
|
return updateDeletedByInference(k._2()._1(), clazz);
|
|
}
|
|
return k._2()._1();
|
|
});
|
|
|
|
sourceEntity = map.union(sc.textFile(dedupRecordPath));
|
|
}
|
|
sourceEntity.saveAsTextFile(outputPath, GzipCodec.class);
|
|
}
|
|
}
|
|
}
|
|
|
|
public boolean mergeRelExists(String basePath, String entity) throws IOException {
|
|
|
|
boolean result = false;
|
|
|
|
FileSystem fileSystem = FileSystem.get(new Configuration());
|
|
FileStatus[] fileStatuses = fileSystem.listStatus(new Path(basePath));
|
|
|
|
for (FileStatus fs : fileStatuses) {
|
|
final Path mergeRelPath = new Path(
|
|
DedupUtility.createMergeRelPath(basePath, fs.getPath().getName(), entity));
|
|
if (fs.isDirectory() && fileSystem.exists(mergeRelPath)) {
|
|
result = true;
|
|
}
|
|
}
|
|
|
|
return result;
|
|
}
|
|
|
|
private static <T extends OafEntity> String updateDeletedByInference(
|
|
final String json, final Class<T> clazz) {
|
|
try {
|
|
Oaf entity = OBJECT_MAPPER.readValue(json, clazz);
|
|
if (entity.getDataInfo() == null)
|
|
entity.setDataInfo(new DataInfo());
|
|
entity.getDataInfo().setDeletedbyinference(true);
|
|
return OBJECT_MAPPER.writeValueAsString(entity);
|
|
} catch (IOException e) {
|
|
throw new RuntimeException("Unable to convert json", e);
|
|
}
|
|
}
|
|
|
|
private static JavaPairRDD<String, String> excludeRootOrgs(JavaPairRDD<String, String> entitiesWithId,
|
|
Dataset<Relation> rel) {
|
|
|
|
JavaPairRDD<String, String> roots = rel
|
|
.where("relClass == 'merges'")
|
|
.select(rel.col("source"))
|
|
.distinct()
|
|
.toJavaRDD()
|
|
.mapToPair(
|
|
(PairFunction<Row, String, String>) r -> new Tuple2<>(r.getString(0), "root"));
|
|
|
|
return entitiesWithId
|
|
.leftOuterJoin(roots)
|
|
.filter(e -> !e._2()._2().isPresent())
|
|
.mapToPair(e -> new Tuple2<>(e._1(), e._2()._1()));
|
|
}
|
|
}
|