This commit is contained in:
parent
7d9fd75020
commit
00c2ca3ee5
|
|
@ -4,17 +4,18 @@ import com.fasterxml.jackson.databind.ObjectMapper;
|
|||
import com.google.gson.Gson;
|
||||
import eu.dnetlib.dhp.TypedRow;
|
||||
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
|
||||
import eu.dnetlib.dhp.projecttoresult.SparkResultToProjectThroughSemRelJob;
|
||||
import eu.dnetlib.dhp.schema.oaf.*;
|
||||
import org.apache.commons.io.IOUtils;
|
||||
import org.apache.hadoop.io.Text;
|
||||
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 scala.Tuple2;
|
||||
|
||||
import java.io.File;
|
||||
import java.util.*;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
|
|
@ -26,10 +27,13 @@ public class SparkResultToCommunityFromOrganization {
|
|||
|
||||
final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResultToCommunityFromOrganization.class.getResourceAsStream("/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_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(SparkResultToCommunityFromOrganization.class.getSimpleName())
|
||||
.master(parser.get("master"))
|
||||
.config(conf)
|
||||
.enableHiveSupport()
|
||||
.getOrCreate();
|
||||
|
||||
|
|
@ -37,83 +41,226 @@ public class SparkResultToCommunityFromOrganization {
|
|||
final String inputPath = parser.get("sourcePath");
|
||||
final String outputPath = "/tmp/provision/propagation/communitytoresult";
|
||||
final OrganizationMap organizationMap = new Gson().fromJson(parser.get("organizationtoresultcommunitymap"), OrganizationMap.class);
|
||||
boolean writeUpdates = TRUE.equals(parser.get("writeUpdate"));
|
||||
boolean saveGraph = TRUE.equals(parser.get("saveGraph"));
|
||||
|
||||
System.out.println(new Gson().toJson(organizationMap));
|
||||
|
||||
createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
|
||||
|
||||
JavaRDD<Relation> relations_rdd_all = sc.textFile(inputPath + "/relation")
|
||||
.map(item -> new ObjectMapper().readValue(item, Relation.class));
|
||||
JavaRDD<Publication> publications_rdd_all = sc.textFile(inputPath + "/publication")
|
||||
.map(item -> new ObjectMapper().readValue(item, Publication.class));
|
||||
JavaRDD<Dataset> dataset_rdd_all = sc.textFile(inputPath + "/dataset")
|
||||
.map(item -> new ObjectMapper().readValue(item, Dataset.class));
|
||||
JavaRDD<OtherResearchProduct> orp_rdd_all = sc.textFile(inputPath + "/otheresearchproduct")
|
||||
.map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class));
|
||||
JavaRDD<Software> software_rdd_all = sc.textFile(inputPath + "/software")
|
||||
.map(item -> new ObjectMapper().readValue(item, Software.class));
|
||||
|
||||
org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(relations_rdd_all.rdd(), Encoders.bean(Relation.class));
|
||||
|
||||
relation.createOrReplaceTempView("relation");
|
||||
// String query = "SELECT source, target" +
|
||||
// " FROM relation " +
|
||||
// " WHERE datainfo.deletedbyinference = false " +
|
||||
// " AND relClass = '" + RELATION_RESULT_ORGANIZATION_REL_CLASS + "'";
|
||||
//
|
||||
// org.apache.spark.sql.Dataset<Row> result_organization = spark.sql(query);
|
||||
// result_organization.createOrReplaceTempView("result_organization");
|
||||
//
|
||||
// query = "SELECT source, target " +
|
||||
// "FROM relation " +
|
||||
// "WHERE datainfo.deletedbyinference = false " +
|
||||
// "AND relClass = '" + RELATION_REPRESENTATIVERESULT_RESULT_CLASS + "'" ;
|
||||
|
||||
String query = "SELECT result_organization.source, result_organization.target, org_set " +
|
||||
"FROM (SELECT source, target " +
|
||||
" FROM relation " +
|
||||
" WHERE datainfo.deletedbyinference = false " +
|
||||
" AND relClass = '" + RELATION_RESULT_ORGANIZATION_REL_CLASS + "') result_organization " +
|
||||
"LEFT JOIN (SELECT source, collect_set(target) org_set " +
|
||||
" FROM relation " +
|
||||
" WHERE datainfo.deletedbyinference = false " +
|
||||
" AND relClass = '" + RELATION_REPRESENTATIVERESULT_RESULT_CLASS + "' " +
|
||||
" GROUP BY source) organization_organization " +
|
||||
"ON result_organization.target = organization_organization.source ";
|
||||
|
||||
org.apache.spark.sql.Dataset<Row> result_organizationset = spark.sql(query);
|
||||
|
||||
JavaPairRDD<String,TypedRow> result_communitySet = result_organizationset.toJavaRDD().map(r -> {
|
||||
String rId = r.getString(0);
|
||||
List<String> orgs = r.getList(2);
|
||||
String oTarget = r.getString(1);
|
||||
TypedRow tp = new TypedRow();
|
||||
if (organizationMap.containsKey(oTarget)) {
|
||||
tp.addAll(organizationMap.get(oTarget));
|
||||
}
|
||||
try{
|
||||
for (String oId : orgs) {
|
||||
if (organizationMap.containsKey(oId)) {
|
||||
tp.addAll(organizationMap.get(oId));
|
||||
}
|
||||
}
|
||||
}
|
||||
catch(Exception e){
|
||||
//System.out.println("organizationTargetID: " + oTarget);
|
||||
}
|
||||
|
||||
if(tp.getAccumulator() == null ){
|
||||
return null;
|
||||
}
|
||||
tp.setSourceId(rId);
|
||||
|
||||
|
||||
File directory = new File(outputPath);
|
||||
return tp;
|
||||
})
|
||||
.filter(tr -> !(tr==null))
|
||||
.mapToPair(toPair()).cache();
|
||||
|
||||
if (!directory.exists()) {
|
||||
directory.mkdirs();
|
||||
if(writeUpdates){
|
||||
result_communitySet.map(c->new ObjectMapper().writeValueAsString(c)).saveAsTextFile(outputPath +"/result_communityset");
|
||||
}
|
||||
|
||||
JavaRDD<Relation> relations = sc.sequenceFile(inputPath + "/relation", Text.class, Text.class)
|
||||
.map(item -> new ObjectMapper().readValue(item._2().toString(), Relation.class)).cache();
|
||||
if(saveGraph){
|
||||
updatePublicationResult(publications_rdd_all, result_communitySet)
|
||||
.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
.saveAsTextFile(outputPath + "/publication");
|
||||
|
||||
updateDatasetResult(dataset_rdd_all, result_communitySet)
|
||||
.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
.saveAsTextFile(outputPath + "/dataset");
|
||||
|
||||
updateORPResult(orp_rdd_all, result_communitySet)
|
||||
.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
.saveAsTextFile(outputPath + "/otherresearchproduct");
|
||||
|
||||
updateSoftwareResult(software_rdd_all, result_communitySet)
|
||||
.map(p -> new ObjectMapper().writeValueAsString(p))
|
||||
.saveAsTextFile(outputPath + "/software");
|
||||
}
|
||||
|
||||
|
||||
//relations between organziations and results
|
||||
JavaPairRDD<String, TypedRow> organization_result = relations
|
||||
.filter(r -> !r.getDataInfo().getDeletedbyinference())
|
||||
.filter(r -> RELATION_RESULT_ORGANIZATION_REL_CLASS.equals(r.getRelClass()) && RELATION_RESULTORGANIZATION_REL_TYPE.equals(r.getRelType()))
|
||||
.map(r -> new TypedRow().setSourceId(r.getTarget()).setTargetId(r.getSource() ))
|
||||
.mapToPair(toPair());
|
||||
// JavaPairRDD<String, TypedRow> organization_result = relations
|
||||
// .filter(r -> !r.getDataInfo().getDeletedbyinference())
|
||||
// .filter(r -> RELATION_RESULT_ORGANIZATION_REL_CLASS.equals(r.getRelClass())
|
||||
// && RELATION_RESULTORGANIZATION_REL_TYPE.equals(r.getRelType()))
|
||||
// .map(r -> {
|
||||
// TypedRow tp = new TypedRow();
|
||||
// tp.setSourceId(r.getTarget());
|
||||
// tp.setTargetId(r.getSource() );
|
||||
// return tp;
|
||||
// })
|
||||
// .mapToPair(toPair());
|
||||
|
||||
//relations between representative organization and merged Id. One relation per merged organization
|
||||
JavaPairRDD<String, TypedRow> organization_organization = relations
|
||||
.filter(r -> !r.getDataInfo().getDeletedbyinference())
|
||||
.filter( r -> RELATION_ORGANIZATIONORGANIZATION_REL_TYPE.equals(r.getRelType()) && RELATION_REPRESENTATIVERESULT_RESULT_CLASS.equals(r.getRelClass()))
|
||||
.map(r -> new TypedRow().setSourceId(r.getSource()).setTargetId(r.getTarget()))
|
||||
.mapToPair(toPair());
|
||||
// JavaPairRDD<String, TypedRow> organization_organization = relations
|
||||
// .filter(r -> !r.getDataInfo().getDeletedbyinference())
|
||||
// .filter( r -> RELATION_ORGANIZATIONORGANIZATION_REL_TYPE.equals(r.getRelType())
|
||||
// && RELATION_REPRESENTATIVERESULT_RESULT_CLASS.equals(r.getRelClass()))
|
||||
// .map(r -> {
|
||||
// TypedRow tp = new TypedRow();
|
||||
// tp.setSourceId(r.getSource());
|
||||
// tp.setTargetId(r.getTarget());
|
||||
// return tp;
|
||||
// })
|
||||
// .mapToPair(toPair());
|
||||
|
||||
//get the original id of the organizations to be checked against the id associated to the communities
|
||||
JavaPairRDD<String, TypedRow> organizationoriginal_result = organization_result.leftOuterJoin(organization_organization)
|
||||
.map(c -> {
|
||||
if (!c._2()._2().isPresent())
|
||||
return c._2()._1();
|
||||
return c._2()._1().setSourceId(c._2()._2().get().getTargetId());
|
||||
})
|
||||
.mapToPair(toPair());
|
||||
// JavaPairRDD<String, TypedRow> organizationoriginal_result = organization_result.leftOuterJoin(organization_organization)
|
||||
// .map(c -> {
|
||||
// if (!c._2()._2().isPresent())
|
||||
// return c._2()._1();
|
||||
// return c._2()._1().setSourceId(c._2()._2().get().getTargetId());
|
||||
// })
|
||||
// .mapToPair(toPair());
|
||||
|
||||
//associates to each result connected to an organization the list of communities related to that organization
|
||||
JavaPairRDD<String, TypedRow> to_add_result_communities = organizationoriginal_result.map(o -> {
|
||||
List<String> communityList = organizationMap.get(o._1());
|
||||
if (communityList.size() == 0)
|
||||
return null;
|
||||
TypedRow tp = o._2();
|
||||
tp.setAccumulator(new HashSet<>(communityList)).setSourceId(tp.getTargetId());
|
||||
return tp;
|
||||
})
|
||||
.filter(r -> !(r == null))
|
||||
.mapToPair(toPair())
|
||||
.reduceByKey((a, b) -> {
|
||||
if (a == null)
|
||||
return b;
|
||||
if (b == null)
|
||||
return a;
|
||||
a.addAll(b.getAccumulator());
|
||||
return a;
|
||||
});
|
||||
// JavaPairRDD<String, TypedRow> to_add_result_communities = organizationoriginal_result.map(o -> {
|
||||
// List<String> communityList = organizationMap.get(o._1());
|
||||
// if (communityList.size() == 0)
|
||||
// return null;
|
||||
// TypedRow tp = o._2();
|
||||
// tp.setAccumulator(new HashSet<>(communityList));
|
||||
// tp.setSourceId(tp.getTargetId());
|
||||
// return tp;
|
||||
// })
|
||||
// .filter(r -> !(r == null))
|
||||
// .mapToPair(toPair())
|
||||
// .reduceByKey((a, b) -> {
|
||||
// if (a == null)
|
||||
// return b;
|
||||
// if (b == null)
|
||||
// return a;
|
||||
// a.addAll(b.getAccumulator());
|
||||
// return a;
|
||||
// });
|
||||
|
||||
|
||||
JavaRDD<Publication> publications = sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
|
||||
.map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class)).cache();
|
||||
JavaRDD<Dataset> datasets = sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)
|
||||
.map(item -> new ObjectMapper().readValue(item._2().toString(), Dataset.class)).cache();
|
||||
JavaRDD<Software> software = sc.sequenceFile(inputPath + "/software", Text.class, Text.class)
|
||||
.map(item -> new ObjectMapper().readValue(item._2().toString(), Software.class)).cache();
|
||||
JavaRDD<OtherResearchProduct> other = sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)
|
||||
.map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class)).cache();
|
||||
|
||||
JavaPairRDD<String, Result> pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
JavaPairRDD<String, Result> dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
JavaPairRDD<String, Result> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
JavaPairRDD<String, Result> orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
|
||||
updateResultForCommunity(pubs, to_add_result_communities, outputPath, "publication", PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME);
|
||||
updateResultForCommunity(dss, to_add_result_communities, outputPath, "dataset", PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME);
|
||||
updateResultForCommunity(sfw, to_add_result_communities, outputPath, "software", PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME);
|
||||
updateResultForCommunity(orp, to_add_result_communities, outputPath, "otherresearchproduct", PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME);
|
||||
// JavaRDD<Publication> publications = sc.sequenceFile(inputPath + "/publication", Text.class, Text.class)
|
||||
// .map(item -> new ObjectMapper().readValue(item._2().toString(), Publication.class)).cache();
|
||||
// JavaRDD<Dataset> datasets = sc.sequenceFile(inputPath + "/dataset", Text.class, Text.class)
|
||||
// .map(item -> new ObjectMapper().readValue(item._2().toString(), Dataset.class)).cache();
|
||||
// JavaRDD<Software> software = sc.sequenceFile(inputPath + "/software", Text.class, Text.class)
|
||||
// .map(item -> new ObjectMapper().readValue(item._2().toString(), Software.class)).cache();
|
||||
// JavaRDD<OtherResearchProduct> other = sc.sequenceFile(inputPath + "/otherresearchproduct", Text.class, Text.class)
|
||||
// .map(item -> new ObjectMapper().readValue(item._2().toString(), OtherResearchProduct.class)).cache();
|
||||
//
|
||||
// JavaPairRDD<String, Result> pubs = publications.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
// JavaPairRDD<String, Result> dss = datasets.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
// JavaPairRDD<String, Result> sfw = software.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
// JavaPairRDD<String, Result> orp = other.mapToPair(p -> new Tuple2<>(p.getId(),p));
|
||||
//
|
||||
// updateResultForCommunity(pubs, to_add_result_communities, outputPath, "publication", PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME);
|
||||
// updateResultForCommunity(dss, to_add_result_communities, outputPath, "dataset", PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME);
|
||||
// updateResultForCommunity(sfw, to_add_result_communities, outputPath, "software", PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME);
|
||||
// updateResultForCommunity(orp, to_add_result_communities, outputPath, "otherresearchproduct", PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME);
|
||||
|
||||
}
|
||||
|
||||
private static JavaRDD<Publication> updatePublicationResult(JavaRDD<Publication> result, JavaPairRDD<String, TypedRow> result_communitySet){
|
||||
JavaRDD<Result> tmp = result.map(r -> (Result)r);
|
||||
return updateResultDataset(tmp, result_communitySet).map(r -> (Publication)r);
|
||||
|
||||
}
|
||||
private static JavaRDD<Dataset> updateDatasetResult(JavaRDD<Dataset> result, JavaPairRDD<String, TypedRow> result_communitySet){
|
||||
JavaRDD<Result> tmp = result.map(r -> (Result)r);
|
||||
return updateResultDataset(tmp, result_communitySet).map(r -> (Dataset) r);
|
||||
|
||||
}
|
||||
private static JavaRDD<OtherResearchProduct> updateORPResult(JavaRDD<OtherResearchProduct> result, JavaPairRDD<String, TypedRow> result_communitySet){
|
||||
JavaRDD<Result> tmp = result.map(r -> (Result)r);
|
||||
return updateResultDataset(tmp, result_communitySet).map(r -> (OtherResearchProduct)r);
|
||||
|
||||
}
|
||||
private static JavaRDD<Software> updateSoftwareResult(JavaRDD<Software> result, JavaPairRDD<String, TypedRow> result_communitySet){
|
||||
JavaRDD<Result> tmp = result.map(r -> (Result)r);
|
||||
return updateResultDataset(tmp, result_communitySet).map(r -> (Software) r);
|
||||
|
||||
}
|
||||
private static JavaRDD<Result> updateResultDataset(JavaRDD<Result> result, JavaPairRDD<String, TypedRow> result_communitySet){
|
||||
return result.mapToPair(p -> new Tuple2<>(p.getId(),p)).leftOuterJoin(result_communitySet)
|
||||
.map(c -> {
|
||||
Result r = c._2()._1();
|
||||
if(c._2()._2().isPresent()){
|
||||
Set<String> communitySet = c._2()._2().get().getAccumulator();
|
||||
List<String> contextList = r.getContext().stream().map(con -> con.getId()).collect(Collectors.toList());
|
||||
for(String cId:communitySet){
|
||||
if(!contextList.contains(cId)){
|
||||
Context newContext = new Context();
|
||||
newContext.setId(cId);
|
||||
newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE,
|
||||
PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME)));
|
||||
r.getContext().add(newContext);
|
||||
}
|
||||
}
|
||||
}
|
||||
return r;
|
||||
});
|
||||
|
||||
}
|
||||
// private static void updateResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult, String outputPath, String type) {
|
||||
// results.leftOuterJoin(toupdateresult)
|
||||
// .map(p -> {
|
||||
|
|
|
|||
Loading…
Reference in New Issue