forked from D-Net/dnet-hadoop
removed file from different propagation
This commit is contained in:
parent
f206ff42d6
commit
70b78a40c7
|
|
@ -1,225 +0,0 @@
|
||||||
|
|
||||||
package eu.dnetlib.dhp.resulttocommunityfromorganization;
|
|
||||||
|
|
||||||
/**
|
|
||||||
* @author miriam.baglioni
|
|
||||||
* @Date 16/10/23
|
|
||||||
*/
|
|
||||||
/**
|
|
||||||
* @author miriam.baglioni
|
|
||||||
* @Date 16/10/23
|
|
||||||
*/
|
|
||||||
import static eu.dnetlib.dhp.PropagationConstant.*;
|
|
||||||
import static eu.dnetlib.dhp.PropagationConstant.OBJECT_MAPPER;
|
|
||||||
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
|
|
||||||
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.hadoop.io.ObjectWritable;
|
|
||||||
import org.apache.hadoop.io.compress.GzipCodec;
|
|
||||||
import org.apache.spark.SparkConf;
|
|
||||||
import org.apache.spark.api.java.function.*;
|
|
||||||
import org.apache.spark.api.java.function.FilterFunction;
|
|
||||||
import org.apache.spark.api.java.function.MapFunction;
|
|
||||||
import org.apache.spark.sql.*;
|
|
||||||
import org.apache.spark.sql.types.DataTypes;
|
|
||||||
import org.apache.spark.sql.types.StructType;
|
|
||||||
import org.slf4j.Logger;
|
|
||||||
import org.slf4j.LoggerFactory;
|
|
||||||
|
|
||||||
import com.fasterxml.jackson.databind.ObjectMapper;
|
|
||||||
import com.google.gson.Gson;
|
|
||||||
|
|
||||||
import eu.dnetlib.dhp.api.Utils;
|
|
||||||
import eu.dnetlib.dhp.api.model.CommunityEntityMap;
|
|
||||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
|
||||||
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
|
||||||
import eu.dnetlib.dhp.schema.oaf.Relation;
|
|
||||||
import scala.Tuple2;
|
|
||||||
|
|
||||||
public class PrepareResultCommunity2 {
|
|
||||||
|
|
||||||
private static final Logger log = LoggerFactory
|
|
||||||
.getLogger(eu.dnetlib.dhp.resulttocommunityfromorganization.PrepareResultCommunitySet.class);
|
|
||||||
|
|
||||||
public static void main(String[] args) throws Exception {
|
|
||||||
String jsonConfiguration = IOUtils
|
|
||||||
.toString(
|
|
||||||
eu.dnetlib.dhp.resulttocommunityfromorganization.PrepareResultCommunitySet.class
|
|
||||||
.getResourceAsStream(
|
|
||||||
"/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json"));
|
|
||||||
|
|
||||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
|
|
||||||
parser.parseArgument(args);
|
|
||||||
|
|
||||||
Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
|
|
||||||
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
|
|
||||||
|
|
||||||
String inputPath = parser.get("sourcePath");
|
|
||||||
log.info("inputPath: {}", inputPath);
|
|
||||||
|
|
||||||
final String outputPath = parser.get("outputPath");
|
|
||||||
log.info("outputPath: {}", outputPath);
|
|
||||||
|
|
||||||
final boolean production = Boolean.valueOf(parser.get("production"));
|
|
||||||
log.info("production: {}", production);
|
|
||||||
|
|
||||||
final CommunityEntityMap organizationMap = Utils.getCommunityOrganization(production);
|
|
||||||
log.info("organizationMap: {}", new Gson().toJson(organizationMap));
|
|
||||||
|
|
||||||
SparkConf conf = new SparkConf();
|
|
||||||
|
|
||||||
runWithSparkSession(
|
|
||||||
conf,
|
|
||||||
isSparkSessionManaged,
|
|
||||||
spark -> {
|
|
||||||
removeOutputDir(spark, outputPath);
|
|
||||||
prepareInfo(spark, inputPath, outputPath, organizationMap);
|
|
||||||
});
|
|
||||||
}
|
|
||||||
|
|
||||||
private static void prepareInfo(
|
|
||||||
SparkSession spark,
|
|
||||||
String inputPath,
|
|
||||||
String outputPath,
|
|
||||||
CommunityEntityMap organizationMap) {
|
|
||||||
|
|
||||||
final StructType structureSchema = new StructType()
|
|
||||||
.add(
|
|
||||||
"dataInfo", new StructType()
|
|
||||||
.add("deletedbyinference", DataTypes.BooleanType)
|
|
||||||
.add("invisible", DataTypes.BooleanType))
|
|
||||||
.add("source", DataTypes.StringType)
|
|
||||||
.add("target", DataTypes.StringType)
|
|
||||||
.add("relClass", DataTypes.StringType);
|
|
||||||
|
|
||||||
readPath(spark, inputPath, Relation.class)
|
|
||||||
.foreach((ForeachFunction<Relation>) r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
|
|
||||||
|
|
||||||
Dataset<Row> resultOrganization = spark
|
|
||||||
.read()
|
|
||||||
.schema(Encoders.bean(Relation.class).schema())
|
|
||||||
.json(inputPath)
|
|
||||||
.filter(
|
|
||||||
"dataInfo.deletedbyinference != true " +
|
|
||||||
"and relClass == '" + ModelConstants.HAS_AUTHOR_INSTITUTION + "'")
|
|
||||||
.select(
|
|
||||||
new Column("source").as("resultId"),
|
|
||||||
new Column("target").as("organizationId"));
|
|
||||||
|
|
||||||
resultOrganization
|
|
||||||
.foreach((ForeachFunction<Row>) r -> System.out.println(new ObjectMapper().writeValueAsString(r)));
|
|
||||||
|
|
||||||
Dataset<Row> organizationOrganization = spark
|
|
||||||
.read()
|
|
||||||
.schema(structureSchema)
|
|
||||||
.json(inputPath)
|
|
||||||
.filter(
|
|
||||||
"dataInfo.deletedbyinference != true " +
|
|
||||||
"and relClass == '" + ModelConstants.MERGES + "'")
|
|
||||||
.select(
|
|
||||||
new Column("source").as("masterOrganization"),
|
|
||||||
new Column("target").as("duplicateOrganization"));
|
|
||||||
|
|
||||||
resultOrganization
|
|
||||||
.joinWith(
|
|
||||||
organizationOrganization, resultOrganization
|
|
||||||
.col("organizationId")
|
|
||||||
.equalTo(organizationOrganization.col("masterOrganization")),
|
|
||||||
"left")
|
|
||||||
.groupByKey(
|
|
||||||
(MapFunction<Tuple2<Row, Row>, String>) t2 -> (String) t2._1().getAs("resultId"), Encoders.STRING())
|
|
||||||
.mapGroups((MapGroupsFunction<String, Tuple2<Row, Row>, ResultCommunityList>) (k, v) -> {
|
|
||||||
ResultCommunityList rcl = new ResultCommunityList();
|
|
||||||
rcl.setResultId(k);
|
|
||||||
ArrayList<String> cl = new ArrayList<>();
|
|
||||||
Tuple2<Row, Row> first = v.next();
|
|
||||||
cl.addAll(organizationMap.get(first._1().getAs("organizationId")));
|
|
||||||
if (Optional.ofNullable(first._2()).isPresent()) {
|
|
||||||
cl.addAll(organizationMap.get(first._2().getAs(("duplicateOrganization"))));
|
|
||||||
}
|
|
||||||
v.forEachRemaining(o -> cl.addAll(organizationMap.get(o._2().getAs("duplicateOrganization"))));
|
|
||||||
if (cl.size() == 0)
|
|
||||||
return null;
|
|
||||||
rcl.setCommunityList(new ArrayList<>(cl.stream().distinct().collect(Collectors.toList())));
|
|
||||||
return rcl;
|
|
||||||
}, Encoders.bean(ResultCommunityList.class))
|
|
||||||
.filter(Objects::nonNull)
|
|
||||||
.write()
|
|
||||||
.mode(SaveMode.Overwrite)
|
|
||||||
.option("compression", "gzip")
|
|
||||||
.json(outputPath);
|
|
||||||
|
|
||||||
// Dataset<Relation> relation = readPath(spark, inputPath, Relation.class)
|
|
||||||
// .filter((FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() );
|
|
||||||
//
|
|
||||||
// relation.createOrReplaceTempView("relation");
|
|
||||||
//
|
|
||||||
// String query = "SELECT result_organization.source resultId, result_organization.target orgId, org_set merges "
|
|
||||||
// + "FROM (SELECT source, target "
|
|
||||||
// + " FROM relation "
|
|
||||||
// + " AND lower(relClass) = '"
|
|
||||||
// + ModelConstants.HAS_AUTHOR_INSTITUTION.toLowerCase()
|
|
||||||
// + "') result_organization "
|
|
||||||
// + "LEFT JOIN (SELECT source, collect_set(target) org_set "
|
|
||||||
// + " FROM relation "
|
|
||||||
// + " AND lower(relClass) = '"
|
|
||||||
// + ModelConstants.MERGES.toLowerCase()
|
|
||||||
// + "' "
|
|
||||||
// + " GROUP BY source) organization_organization "
|
|
||||||
// + "ON result_organization.target = organization_organization.source ";
|
|
||||||
//
|
|
||||||
// Dataset<ResultOrganizations> result_organizationset = spark
|
|
||||||
// .sql(query)
|
|
||||||
// .as(Encoders.bean(ResultOrganizations.class));
|
|
||||||
//
|
|
||||||
// result_organizationset
|
|
||||||
// .map(mapResultCommunityFn(organizationMap), Encoders.bean(ResultCommunityList.class))
|
|
||||||
// .filter(Objects::nonNull)
|
|
||||||
// .toJavaRDD()
|
|
||||||
// .mapToPair(value -> new Tuple2<>(value.getResultId(), value))
|
|
||||||
// .reduceByKey((a, b) -> {
|
|
||||||
// ArrayList<String> cl = a.getCommunityList();
|
|
||||||
// b.getCommunityList().stream().forEach(s -> {
|
|
||||||
// if (!cl.contains(s)) {
|
|
||||||
// cl.add(s);
|
|
||||||
// }
|
|
||||||
// });
|
|
||||||
// a.setCommunityList(cl);
|
|
||||||
// return a;
|
|
||||||
// })
|
|
||||||
// .map(value -> OBJECT_MAPPER.writeValueAsString(value._2()))
|
|
||||||
// .saveAsTextFile(outputPath, GzipCodec.class);
|
|
||||||
}
|
|
||||||
|
|
||||||
private static MapFunction<ResultOrganizations, ResultCommunityList> mapResultCommunityFn(
|
|
||||||
CommunityEntityMap organizationMap) {
|
|
||||||
return value -> {
|
|
||||||
String rId = value.getResultId();
|
|
||||||
Optional<List<String>> orgs = Optional.ofNullable(value.getMerges());
|
|
||||||
String oTarget = value.getOrgId();
|
|
||||||
Set<String> communitySet = new HashSet<>();
|
|
||||||
if (organizationMap.containsKey(oTarget)) {
|
|
||||||
communitySet.addAll(organizationMap.get(oTarget));
|
|
||||||
}
|
|
||||||
if (orgs.isPresent())
|
|
||||||
for (String oId : orgs.get()) {
|
|
||||||
if (organizationMap.containsKey(oId)) {
|
|
||||||
communitySet.addAll(organizationMap.get(oId));
|
|
||||||
}
|
|
||||||
}
|
|
||||||
if (!communitySet.isEmpty()) {
|
|
||||||
ResultCommunityList rcl = new ResultCommunityList();
|
|
||||||
rcl.setResultId(rId);
|
|
||||||
ArrayList<String> communityList = new ArrayList<>();
|
|
||||||
communityList.addAll(communitySet);
|
|
||||||
rcl.setCommunityList(communityList);
|
|
||||||
return rcl;
|
|
||||||
}
|
|
||||||
return null;
|
|
||||||
};
|
|
||||||
}
|
|
||||||
}
|
|
||||||
Loading…
Reference in New Issue