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removed file from different propagation

This commit is contained in:
Miriam Baglioni 2023-10-20 15:50:49 +02:00
parent f206ff42d6
commit 70b78a40c7
1 changed files with 0 additions and 225 deletions

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@ -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;
};
}
}