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preparation phase for the propagation of community to result from organization

This commit is contained in:
Miriam Baglioni 2020-04-16 18:43:55 +02:00
parent a9120164aa
commit 3fd9d6b02f
1 changed files with 117 additions and 1 deletions

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@ -1,4 +1,120 @@
package eu.dnetlib.dhp.resulttocommunityfromorganization;
public class PrepareInfo {
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.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1;
import eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob3;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.JavaRDD;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.*;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.util.*;
import static eu.dnetlib.dhp.PropagationConstant.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
public class PrepareResultCommunitySet {
private static final Logger log = LoggerFactory.getLogger(PrepareResultCommunitySet.class);
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils.toString(PrepareResultCommunitySet.class
.getResourceAsStream("/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_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 OrganizationMap organizationMap = new Gson().fromJson(parser.get("organizationtoresultcommunitymap"), OrganizationMap.class);
log.info("organizationMap: {}", new Gson().toJson(organizationMap));
SparkConf conf = new SparkConf();
conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
runWithSparkHiveSession(conf, isSparkSessionManaged,
spark -> {
if (isTest(parser)) {
removeOutputDir(spark, outputPath);
}
prepareInfo(spark, inputPath, outputPath, organizationMap);
});
}
private static void prepareInfo(SparkSession spark, String inputPath, String outputPath, OrganizationMap organizationMap) {
Dataset<Relation> relation = readRelations(spark, inputPath);
relation.createOrReplaceTempView("relation");
String query = "SELECT result_organization.source resultId, result_organization.target orgId, org_set merges " +
"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<ResultOrganizations> result_organizationset = spark.sql(query)
.as(Encoders.bean(ResultOrganizations.class));
result_organizationset
.map(value -> {
String rId = value.getResultId();
List<String> orgs = value.getMerges();
String oTarget = value.getOrgId();
Set<String> communitySet = new HashSet<>();
if (organizationMap.containsKey(oTarget)) {
communitySet.addAll(organizationMap.get(oTarget));
}
try{
for (String oId : orgs) {
if (organizationMap.containsKey(oId)) {
communitySet.addAll(organizationMap.get(oId));
}
}
}catch(Exception e){
}
if (communitySet.size() > 0){
ResultCommunityList rcl = new ResultCommunityList();
rcl.setResultId(rId);
ArrayList<String> communityList = new ArrayList<>();
communityList.addAll(communitySet);
rcl.setCommunityList(communityList);
return rcl;
}
return null;
}, Encoders.bean(ResultCommunityList.class))
.filter(r -> r!= null)
.toJSON()
.write()
.mode(SaveMode.Overwrite)
.option("compression", "gzip")
.text(outputPath);
}
}