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new business logic for the actual propagation. It exploits previously computed information

This commit is contained in:
Miriam Baglioni 2020-04-15 12:25:44 +02:00
parent 6a377a7582
commit 473d17767c
1 changed files with 189 additions and 401 deletions

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@ -1,178 +1,202 @@
package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
import eu.dnetlib.dhp.TypedRow;
import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.countrypropagation.DatasourceCountry;
import eu.dnetlib.dhp.countrypropagation.ResultCountrySet;
import eu.dnetlib.dhp.countrypropagation.SparkCountryPropagationJob2;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.io.IOUtils;
import org.apache.hadoop.fs.FileSystem;
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.Row;
import org.apache.spark.sql.SparkSession;
import org.apache.hadoop.io.Text;
import com.fasterxml.jackson.databind.ObjectMapper;
import java.io.File;
import java.util.*;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.spark.api.java.function.FlatMapFunction;
import org.apache.spark.broadcast.Broadcast;
import org.apache.spark.sql.*;
import org.apache.spark.sql.Dataset;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import scala.Option;
import scala.Tuple2;
import static eu.dnetlib.dhp.PropagationConstant.*;
import java.util.*;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
public class SparkResultToOrganizationFromIstRepoJob2 {
private static final Logger log = LoggerFactory.getLogger(SparkResultToOrganizationFromIstRepoJob2.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public class SparkResultToOrganizationFromIstRepoJob {
public static void main(String[] args) throws Exception {
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResultToOrganizationFromIstRepoJob.class.getResourceAsStream("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_propagationresulaffiliationfrominstrepo_parameters.json")));
String jsonConfiguration = IOUtils.toString(SparkCountryPropagationJob2.class
.getResourceAsStream("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_propagationresulaffiliationfrominstrepo_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 String datasourceorganization = parser.get("datasourceOrganizationPath");
log.info("datasourceOrganizationPath: {}", datasourceorganization);
final String alreadylinked = parser.get("alreadyLinkedPath");
log.info("alreadyLinkedPath: {}", alreadylinked);
final String resultorganizationsetpath = parser.get("resultOrganizationsetPath");
log.info("resultOrganizationsetPath: {}", resultorganizationsetpath);
final String resultClassName = parser.get("resultTableName");
log.info("resultTableName: {}", resultClassName);
final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
log.info("resultType: {}", resultType);
final Boolean writeUpdates = Optional
.ofNullable(parser.get("writeUpdate"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("writeUpdate: {}", writeUpdates);
final Boolean saveGraph = Optional
.ofNullable(parser.get("saveGraph"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("saveGraph: {}", saveGraph);
Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
final SparkSession spark = SparkSession
.builder()
.appName(SparkResultToOrganizationFromIstRepoJob.class.getSimpleName())
.master(parser.get("master"))
.config(conf)
.enableHiveSupport()
.getOrCreate();
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
final String inputPath = parser.get("sourcePath");
final String outputPath = "/tmp/provision/propagation/resulttoorganizationfrominstitutionalrepositories";
createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
org.apache.spark.sql.Dataset<Datasource> datasource = spark.createDataset(sc.textFile(inputPath + "/datasource")
.map(item -> new ObjectMapper().readValue(item, Datasource.class)).rdd(), Encoders.bean(Datasource.class));
org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
.map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
org.apache.spark.sql.Dataset<Organization> organization = spark.createDataset(sc.textFile(inputPath + "/organization")
.map(item -> new ObjectMapper().readValue(item, Organization.class)).rdd(), Encoders.bean(Organization.class));
datasource.createOrReplaceTempView("datasource");
relation.createOrReplaceTempView("relation");
organization.createOrReplaceTempView("organization");
String query = "SELECT source ds, target org " +
"FROM ( SELECT id " +
"FROM datasource " +
"WHERE datasourcetype.classid = 'pubsrepository::institutional' " +
"AND datainfo.deletedbyinference = false ) d " +
"JOIN ( SELECT source, target " +
"FROM relation " +
"WHERE relclass = 'provides' " +
"AND datainfo.deletedbyinference = false ) rel " +
"ON d.id = rel.source ";
org.apache.spark.sql.Dataset<Row> rels = spark.sql(query);
rels.createOrReplaceTempView("rels");
org.apache.spark.sql.Dataset<Dataset> dataset = spark.createDataset(sc.textFile(inputPath + "/dataset")
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Dataset.class)).rdd(),
Encoders.bean(eu.dnetlib.dhp.schema.oaf.Dataset.class));
org.apache.spark.sql.Dataset<OtherResearchProduct> other = spark.createDataset(sc.textFile(inputPath + "/otherresearchproduct")
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class)).rdd(),
Encoders.bean(eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class));
org.apache.spark.sql.Dataset<Software> software = spark.createDataset(sc.textFile(inputPath + "/software")
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Software.class)).rdd(),
Encoders.bean(eu.dnetlib.dhp.schema.oaf.Software.class));
org.apache.spark.sql.Dataset<Publication> publication = spark.createDataset(sc.textFile(inputPath + "/publication")
.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Publication.class)).rdd(),
Encoders.bean(eu.dnetlib.dhp.schema.oaf.Publication.class));
software.createOrReplaceTempView("software");
final JavaRDD<Row> toupdateresultsoftware = propagateOnResult(spark, "software");
dataset.createOrReplaceTempView("dataset");
final JavaRDD<Row> toupdateresultdataset = propagateOnResult(spark, "dataset");
other.createOrReplaceTempView("other");
final JavaRDD<Row> toupdateresultother = propagateOnResult(spark, "other");
publication.createOrReplaceTempView("publication");
final JavaRDD<Row> toupdateresultpublication = propagateOnResult(spark, "publication");
writeUpdates(toupdateresultsoftware, toupdateresultdataset, toupdateresultother, toupdateresultpublication, outputPath);
query = "Select source resultId, collect_set(target) org_list " +
"from relation " +
"where datainfo.deletedbyinference = false " +
"and relClass = '" + RELATION_RESULT_ORGANIZATION_REL_CLASS +"' " +
"group by source";
JavaRDD<Row> result_orglist = spark.sql(query).toJavaRDD();
JavaPairRDD<String, List<Object>> toupdateunion = toupdateresultdataset.mapToPair(d -> new Tuple2<>(d.getString(0), d.getList(1)))
.union(toupdateresultother.mapToPair(o -> new Tuple2<>(o.getString(0), o.getList(1))))
.union(toupdateresultpublication.mapToPair(p -> new Tuple2<>(p.getString(0), p.getList(1))))
.union(toupdateresultsoftware.mapToPair(s -> new Tuple2<>(s.getString(0), s.getList(1))));
JavaRDD<Relation> new_rels = getNewRels(result_orglist.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1))),
toupdateunion);
sc.textFile(inputPath + "/relation")
.map(item -> new ObjectMapper().readValue(item, Relation.class))
.union(new_rels)
.map(r -> new ObjectMapper().writeValueAsString(r))
.saveAsTextFile(outputPath + "/relation");
runWithSparkHiveSession(conf, isSparkSessionManaged,
spark -> {
if(isTest(parser)) {
removeOutputDir(spark, outputPath);
}
private static JavaRDD<Relation> getNewRels(JavaPairRDD<String, List<String>> relationOrgs, JavaPairRDD <String, List<Object>> newRels){
return newRels
.leftOuterJoin(relationOrgs)
.flatMap(c -> {
List<Object> toAddOrgs = new ArrayList<>();
toAddOrgs.addAll(c._2()._1());
if (c._2()._2().isPresent()) {
Set<String> originalOrgs = new HashSet<>();
originalOrgs.addAll(c._2()._2().get());
for (Object oId : originalOrgs) {
if (toAddOrgs.contains(oId)) {
toAddOrgs.remove(oId);
}
}
}
List<Relation> relationList = new ArrayList<>();
String resId = c._1();
for (Object org : toAddOrgs) {
relationList.add(getRelation((String)org, resId, RELATION_ORGANIZATION_RESULT_REL_CLASS,
RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
relationList.add(getRelation(resId, (String)org, RELATION_RESULT_ORGANIZATION_REL_CLASS,
RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
}
return relationList.iterator();
execPropagation(spark, datasourceorganization, alreadylinked, inputPath, outputPath, resultClazz, resultType,
writeUpdates, saveGraph);
});
}
private static void writeUpdates(JavaRDD<Row> toupdateresultsoftware, JavaRDD<Row> toupdateresultdataset, JavaRDD<Row> toupdateresultother, JavaRDD<Row> toupdateresultpublication, String outputPath) {
createUpdateForRelationWrite(toupdateresultsoftware, outputPath, "update_software");
createUpdateForRelationWrite(toupdateresultdataset, outputPath, "update_dataset");
createUpdateForRelationWrite(toupdateresultother, outputPath, "update_other");
createUpdateForRelationWrite(toupdateresultpublication, outputPath, "update_publication");
}
private static void createUpdateForRelationWrite(JavaRDD<Row> toupdaterelation, String outputPath, String update_type) {
private static void execPropagation(SparkSession spark, String datasourceorganization, String alreadylinked, String inputPath,
String outputPath, Class<? extends Result> resultClazz, String resultType,
Boolean writeUpdates, Boolean saveGraph) {
final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
org.apache.spark.sql.Dataset<DatasourceOrganization> datasourceorganizationassoc =
readAssocDatasourceOrganization(spark, datasourceorganization);
//broadcasting the result of the preparation step
Broadcast<org.apache.spark.sql.Dataset<DatasourceOrganization>> broadcast_datasourceorganizationassoc =
sc.broadcast(datasourceorganizationassoc);
org.apache.spark.sql.Dataset<ResultOrganizationSet> potentialUpdates = getPotentialRelations(spark, inputPath, resultClazz,
broadcast_datasourceorganizationassoc).as(Encoders.bean(ResultOrganizationSet.class));
if(writeUpdates){
createUpdateForRelationWrite(potentialUpdates, outputPath + "/" + resultType);
}
if(saveGraph){
getNewRelations(spark
.read()
.textFile(alreadylinked)
.map(value -> OBJECT_MAPPER.readValue(value, ResultOrganizationSet.class),
Encoders.bean(ResultOrganizationSet.class)), potentialUpdates);
}
}
private static Dataset<Relation> getNewRelations(Dataset<ResultOrganizationSet> alreadyLinked, Dataset<ResultOrganizationSet> potentialUpdates) {
return potentialUpdates
.joinWith(alreadyLinked, potentialUpdates.col("resultId")
.equalTo(alreadyLinked.col("resultId")), "left_outer")
.flatMap((FlatMapFunction<Tuple2<ResultOrganizationSet, ResultOrganizationSet>, Relation>) value -> {
List<Relation> new_relations = new ArrayList<>();
ResultOrganizationSet potential_update = value._1();
Optional<ResultOrganizationSet> already_linked = Optional.ofNullable(value._2());
List<String> organization_list = potential_update.getOrganizationSet();
if(already_linked.isPresent()){
already_linked.get().getOrganizationSet()
.stream()
.forEach(rId -> {
if (organization_list.contains(rId)) {
organization_list.remove(rId);
}
});
}
String resultId = potential_update.getResultId();
organization_list
.stream()
.forEach(orgId -> {
new_relations.add(getRelation(orgId, resultId, RELATION_ORGANIZATION_RESULT_REL_CLASS, RELATION_RESULTORGANIZATION_REL_TYPE,
RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID,
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
new_relations.add(getRelation(resultId, orgId, RELATION_RESULT_ORGANIZATION_REL_CLASS, RELATION_RESULTORGANIZATION_REL_TYPE,
RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID,
PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
}
);
return new_relations.iterator();
}
,Encoders.bean(Relation.class));
}
private static <R extends Result> org.apache.spark.sql.Dataset<ResultOrganizationSet> getPotentialRelations(SparkSession spark,
String inputPath,
Class<R> resultClazz,
Broadcast<org.apache.spark.sql.Dataset<DatasourceOrganization>> broadcast_datasourceorganizationassoc) {
org.apache.spark.sql.Dataset<R> result = readPathEntity(spark, inputPath, resultClazz);
result.createOrReplaceTempView("result");
createCfHbforresult(spark);
return organizationPropagationAssoc(spark, broadcast_datasourceorganizationassoc);
}
private static org.apache.spark.sql.Dataset<DatasourceOrganization> readAssocDatasourceOrganization(SparkSession spark,
String datasourcecountryorganization) {
return spark
.read()
.textFile(datasourcecountryorganization)
.map(value -> OBJECT_MAPPER.readValue(value, DatasourceOrganization.class), Encoders.bean(DatasourceOrganization.class));
}
private static void createUpdateForRelationWrite(Dataset<ResultOrganizationSet> toupdaterelation, String outputPath) {
toupdaterelation.flatMap(s -> {
List<Relation> relationList = new ArrayList<>();
List<String> orgs = s.getList(1);
String resId = s.getString(0);
List<String> orgs = s.getOrganizationSet();
String resId = s.getResultId();
for (String org : orgs) {
relationList.add(getRelation(org, resId, RELATION_ORGANIZATION_RESULT_REL_CLASS,
RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
@ -183,267 +207,31 @@ public class SparkResultToOrganizationFromIstRepoJob {
}
return relationList.iterator();
}).map(s -> new ObjectMapper().writeValueAsString(s)).saveAsTextFile(outputPath + "/" + update_type);
}, Encoders.bean(Relation.class))
.toJSON()
.write()
.mode(SaveMode.Overwrite)
.option("compression","gzip")
.text(outputPath)
;
}
private static JavaRDD<Row> propagateOnResult(SparkSession spark, String table) {
String query;
query = "SELECT id, inst.collectedfrom.key cf , inst.hostedby.key hb " +
"FROM ( SELECT id, instance " +
"FROM " + table +
" WHERE datainfo.deletedbyinference = false) ds " +
"LATERAL VIEW EXPLODE(instance) i AS inst";
org.apache.spark.sql.Dataset<Row> cfhb = spark.sql(query);
cfhb.createOrReplaceTempView("cfhb");
return organizationPropagationAssoc(spark, "cfhb").toJavaRDD();
}
private static org.apache.spark.sql.Dataset<Row> organizationPropagationAssoc(SparkSession spark, String cfhbTable){
String query = "SELECT id, collect_set(org) org "+
"FROM ( SELECT id, org " +
private static org.apache.spark.sql.Dataset<ResultOrganizationSet> organizationPropagationAssoc(SparkSession spark, Broadcast<org.apache.spark.sql.Dataset<DatasourceOrganization>> broadcast_datasourceorganizationassoc){
org.apache.spark.sql.Dataset<DatasourceOrganization> datasourceorganization = broadcast_datasourceorganizationassoc.value();
datasourceorganization.createOrReplaceTempView("rels");
String query = "SELECT id resultId, collect_set(organizationId) organizationSet "+
"FROM ( SELECT id, organizationId " +
"FROM rels " +
"JOIN " + cfhbTable +
" ON cf = ds " +
"JOIN cfhb " +
" ON cf = datasourceId " +
"UNION ALL " +
"SELECT id , org " +
"SELECT id , organizationId " +
"FROM rels " +
"JOIN " + cfhbTable +
" ON hb = ds ) tmp " +
"JOIN cfhb " +
" ON hb = datasourceId ) tmp " +
"GROUP BY id";
return spark.sql(query);
return spark.sql(query).as(Encoders.bean(ResultOrganizationSet.class));
}
}
//package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
//
//import eu.dnetlib.dhp.TypedRow;
//import eu.dnetlib.dhp.application.ArgumentApplicationParser;
//import org.apache.commons.io.IOUtils;
//import org.apache.hadoop.fs.FileSystem;
//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.Row;
//import org.apache.spark.sql.SparkSession;
//import org.apache.hadoop.io.Text;
//import com.fasterxml.jackson.databind.ObjectMapper;
//import java.io.File;
//import java.util.ArrayList;
//import java.util.Arrays;
//import java.util.List;
//import java.util.Set;
//
//import eu.dnetlib.dhp.schema.oaf.*;
//import scala.Tuple2;
//
//import static eu.dnetlib.dhp.PropagationConstant.*;
//
//public class SparkResultToOrganizationFromIstRepoJob {
// public static void main(String[] args) throws Exception {
//
// final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResultToOrganizationFromIstRepoJob.class.getResourceAsStream("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_propagationresulaffiliationfrominstrepo_parameters.json")));
// parser.parseArgument(args);
// SparkConf conf = new SparkConf();
// conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
// final SparkSession spark = SparkSession
// .builder()
// .appName(SparkResultToOrganizationFromIstRepoJob.class.getSimpleName())
// .master(parser.get("master"))
// .config(conf)
// .enableHiveSupport()
// .getOrCreate();
//
// final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
// final String inputPath = parser.get("sourcePath");
// final String outputPath = "/tmp/provision/propagation/resulttoorganizationfrominstitutionalrepositories";
//
// createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
//
// org.apache.spark.sql.Dataset<Datasource> datasource = spark.createDataset(sc.textFile(inputPath + "/datasource")
// .map(item -> new ObjectMapper().readValue(item, Datasource.class))
// .rdd(), Encoders.bean(Datasource.class));
//
// JavaRDD<Relation> relation_rdd_all = sc.textFile(inputPath + "/relation")
// .map(item -> new ObjectMapper().readValue(item, Relation.class));
// JavaRDD<Relation> relation_rdd = relation_rdd_all.filter(r -> !r.getDataInfo().getDeletedbyinference()).cache();
//
// org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(relation_rdd.rdd(), Encoders.bean(Relation.class));
//
// org.apache.spark.sql.Dataset<Organization> organization = spark.createDataset(sc.textFile(inputPath + "/organziation")
// .map(item -> new ObjectMapper().readValue(item, Organization.class)).rdd(), Encoders.bean(Organization.class));
//
// datasource.createOrReplaceTempView("datasource");
// relation.createOrReplaceTempView("relation");
// organization.createOrReplaceTempView("organization");
//
// String query = "SELECT source ds, target org " +
// "FROM ( SELECT id " +
// "FROM datasource " +
// "WHERE datasourcetype.classid = 'pubsrepository::institutional' " +
// "AND datainfo.deletedbyinference = false ) d " +
// "JOIN ( SELECT source, target " +
// "FROM relation " +
// "WHERE relclass = 'provides' " +
// "AND datainfo.deletedbyinference = false ) rel " +
// "ON d.id = rel.source ";
//
// org.apache.spark.sql.Dataset<Row> rels = spark.sql(query);
// rels.createOrReplaceTempView("rels");
//
// org.apache.spark.sql.Dataset<Dataset> dataset = spark.createDataset(sc.textFile(inputPath + "/dataset")
// .map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Dataset.class)).rdd(),
// Encoders.bean(eu.dnetlib.dhp.schema.oaf.Dataset.class));
//
// org.apache.spark.sql.Dataset<OtherResearchProduct> other = spark.createDataset(sc.textFile(inputPath + "/otherresearchproduct")
// .map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class)).rdd(),
// Encoders.bean(eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class));
//
// org.apache.spark.sql.Dataset<Software> software = spark.createDataset(sc.textFile(inputPath + "/software")
// .map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Software.class)).rdd(),
// Encoders.bean(eu.dnetlib.dhp.schema.oaf.Software.class));
//
// org.apache.spark.sql.Dataset<Publication> publication = spark.createDataset(sc.textFile(inputPath + "/publication")
// .map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Publication.class)).rdd(),
// Encoders.bean(eu.dnetlib.dhp.schema.oaf.Publication.class));
//
//
// software.createOrReplaceTempView("software");
// final JavaRDD<Row> toupdateresultsoftware = propagateOnResult(spark, "software");
//
// dataset.createOrReplaceTempView("dataset");
// final JavaRDD<Row> toupdateresultdataset = propagateOnResult(spark, "dataset");
//
// other.createOrReplaceTempView("other");
// final JavaRDD<Row> toupdateresultother = propagateOnResult(spark, "other");
//
// publication.createOrReplaceTempView("publication");
// final JavaRDD<Row> toupdateresultpublication = propagateOnResult(spark, "publication");
//
// writeUpdates(toupdateresultsoftware, toupdateresultdataset, toupdateresultother, toupdateresultpublication, outputPath);
//
// JavaPairRDD<String, TypedRow> relation_rdd_pair = relation_rdd
// .filter(r -> RELATION_RESULT_ORGANIZATION_REL_CLASS.equals(r.getRelClass()))
// .map(r -> {
// TypedRow tp = new TypedRow();
// tp.setSourceId(r.getSource());
// tp.add(r.getTarget());
// return tp;
// }).mapToPair(toPair())
// .reduceByKey((a, b) -> {
// if (a == null) {
// return b;
// }
// if (b == null) {
// return a;
// }
//
// a.addAll(b.getAccumulator());
// return a;
// }).cache();
//
//
// JavaRDD<Relation> new_rels = getNewRels(relation_rdd_pair,
// toupdateresultother.mapToPair(s -> new Tuple2<>(s.getString(0), s.getList(1))))
// .union(getNewRels(relation_rdd_pair,
// toupdateresultsoftware.mapToPair(s -> new Tuple2<>(s.getString(0), s.getList(1)))))
// .union(getNewRels(relation_rdd_pair,
// toupdateresultdataset.mapToPair(s -> new Tuple2<>(s.getString(0), s.getList(1)))))
// .union(getNewRels(relation_rdd_pair,
// toupdateresultpublication.mapToPair(s -> new Tuple2<>(s.getString(0), s.getList(1)))));
//
//
// relation_rdd_all.union(new_rels).map(r -> new ObjectMapper().writeValueAsString(r))
// .saveAsTextFile(outputPath + "/relation");
//
// }
//
// private static JavaRDD<Relation> getNewRels(JavaPairRDD<String, TypedRow> relation_rdd_pair, JavaPairRDD <String, List<String>> newRels){
// return newRels//.mapToPair(s -> new Tuple2<>(s.getString(0), s.getList(1)))
// .leftOuterJoin(relation_rdd_pair)
// .flatMap(c -> {
// List<String> toAddOrgs = c._2()._1();
// if (c._2()._2().isPresent()) {
// Set<String> originalOrgs = c._2()._2().get().getAccumulator();
// for (String oId : toAddOrgs) {
// if (originalOrgs.contains(oId)) {
// toAddOrgs.remove(oId);
// }
// }
// }
// List<Relation> relationList = new ArrayList<>();
// String resId = c._1();
// for (String org : toAddOrgs) {
// relationList.add(getRelation(org, resId, RELATION_ORGANIZATION_RESULT_REL_CLASS,
// RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
// PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
// relationList.add(getRelation(resId, org, RELATION_RESULT_ORGANIZATION_REL_CLASS,
// RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
// PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
//
// }
// return relationList.iterator();
// });
//
// }
//
// private static void writeUpdates(JavaRDD<Row> toupdateresultsoftware, JavaRDD<Row> toupdateresultdataset, JavaRDD<Row> toupdateresultother, JavaRDD<Row> toupdateresultpublication, String outputPath) {
// createUpdateForRelationWrite(toupdateresultsoftware, outputPath, "update_software");
// createUpdateForRelationWrite(toupdateresultdataset, outputPath, "update_dataset");
// createUpdateForRelationWrite(toupdateresultother, outputPath, "update_other");
// createUpdateForRelationWrite(toupdateresultpublication, outputPath, "update_publication");
//
// }
//
// private static void createUpdateForRelationWrite(JavaRDD<Row> toupdaterelation, String outputPath, String update_type) {
// toupdaterelation.flatMap(s -> {
// List<Relation> relationList = new ArrayList<>();
// List<String> orgs = s.getList(1);
// String resId = s.getString(0);
// for (String org : orgs) {
// relationList.add(getRelation(org, resId, RELATION_ORGANIZATION_RESULT_REL_CLASS,
// RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
// PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
// relationList.add(getRelation(resId, org, RELATION_RESULT_ORGANIZATION_REL_CLASS,
// RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
// PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
//
// }
// return relationList.iterator();
// }).map(s -> new ObjectMapper().writeValueAsString(s)).saveAsTextFile(outputPath + "/" + update_type);
// }
//
// private static JavaRDD<Row> propagateOnResult(SparkSession spark, String table) {
// String query;
// query = "SELECT id, inst.collectedfrom.key cf , inst.hostedby.key hb " +
// "FROM ( SELECT id, instance " +
// "FROM " + table +
// " WHERE datainfo.deletedbyinference = false) ds " +
// "LATERAL VIEW EXPLODE(instance) i AS inst";
// org.apache.spark.sql.Dataset<Row> cfhb = spark.sql(query);
// cfhb.createOrReplaceTempView("cfhb");
//
// return organizationPropagationAssoc(spark, "cfhb").toJavaRDD();
//
// }
//
// private static org.apache.spark.sql.Dataset<Row> organizationPropagationAssoc(SparkSession spark, String cfhbTable){
// String query = "SELECT id, collect_set(org) org "+
// "FROM ( SELECT id, org " +
// "FROM rels " +
// "JOIN " + cfhbTable +
// " ON cf = ds " +
// "UNION ALL " +
// "SELECT id , org " +
// "FROM rels " +
// "JOIN " + cfhbTable +
// " ON hb = ds ) tmp " +
// "GROUP BY id";
// return spark.sql(query);
// }
//
//}