refactoring
This commit is contained in:
parent
44fab140de
commit
edb00db86a
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@ -6,13 +6,13 @@ import java.util.List;
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public class OrganizationMap extends HashMap<String, List<String>> {
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public OrganizationMap(){
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public OrganizationMap() {
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super();
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}
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public List<String> get(String key){
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public List<String> get(String key) {
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if (super.get(key) == null){
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if (super.get(key) == null) {
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return new ArrayList<>();
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}
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return super.get(key);
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@ -1,20 +1,19 @@
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package eu.dnetlib.dhp.resulttocommunityfromorganization;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import com.google.gson.Gson;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import java.util.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.sql.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.util.*;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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public class PrepareResultCommunitySet {
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private static final Logger log = LoggerFactory.getLogger(PrepareResultCommunitySet.class);
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@ -22,11 +21,12 @@ public class PrepareResultCommunitySet {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils.toString(PrepareResultCommunitySet.class
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.getResourceAsStream("/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json"));
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String jsonConfiguration =
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IOUtils.toString(
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PrepareResultCommunitySet.class.getResourceAsStream(
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"/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -39,76 +39,91 @@ public class PrepareResultCommunitySet {
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final OrganizationMap organizationMap = new Gson().fromJson(parser.get("organizationtoresultcommunitymap"), OrganizationMap.class);
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final OrganizationMap organizationMap =
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new Gson()
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.fromJson(
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parser.get("organizationtoresultcommunitymap"),
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OrganizationMap.class);
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log.info("organizationMap: {}", new Gson().toJson(organizationMap));
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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runWithSparkHiveSession(conf, isSparkSessionManaged,
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runWithSparkHiveSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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if (isTest(parser)) {
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removeOutputDir(spark, outputPath);
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}
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prepareInfo(spark, inputPath, outputPath, organizationMap);
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prepareInfo(spark, inputPath, outputPath, organizationMap);
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});
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}
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private static void prepareInfo(SparkSession spark, String inputPath, String outputPath, OrganizationMap organizationMap) {
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private static void prepareInfo(
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SparkSession spark,
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String inputPath,
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String outputPath,
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OrganizationMap organizationMap) {
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Dataset<Relation> relation = readRelations(spark, inputPath);
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relation.createOrReplaceTempView("relation");
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String query = "SELECT result_organization.source resultId, result_organization.target orgId, org_set merges " +
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"FROM (SELECT source, target " +
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" FROM relation " +
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" WHERE datainfo.deletedbyinference = false " +
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" AND relClass = '" + RELATION_RESULT_ORGANIZATION_REL_CLASS + "') result_organization " +
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"LEFT JOIN (SELECT source, collect_set(target) org_set " +
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" FROM relation " +
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" WHERE datainfo.deletedbyinference = false " +
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" AND relClass = '" + RELATION_REPRESENTATIVERESULT_RESULT_CLASS + "' " +
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" GROUP BY source) organization_organization " +
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"ON result_organization.target = organization_organization.source ";
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String query =
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"SELECT result_organization.source resultId, result_organization.target orgId, org_set merges "
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+ "FROM (SELECT source, target "
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+ " FROM relation "
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+ " WHERE datainfo.deletedbyinference = false "
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+ " AND relClass = '"
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+ RELATION_RESULT_ORGANIZATION_REL_CLASS
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+ "') result_organization "
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+ "LEFT JOIN (SELECT source, collect_set(target) org_set "
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+ " FROM relation "
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+ " WHERE datainfo.deletedbyinference = false "
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+ " AND relClass = '"
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+ RELATION_REPRESENTATIVERESULT_RESULT_CLASS
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+ "' "
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+ " GROUP BY source) organization_organization "
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+ "ON result_organization.target = organization_organization.source ";
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org.apache.spark.sql.Dataset<ResultOrganizations> result_organizationset = spark.sql(query)
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.as(Encoders.bean(ResultOrganizations.class));
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org.apache.spark.sql.Dataset<ResultOrganizations> result_organizationset =
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spark.sql(query).as(Encoders.bean(ResultOrganizations.class));
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result_organizationset
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.map(value -> {
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String rId = value.getResultId();
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List<String> orgs = value.getMerges();
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String oTarget = value.getOrgId();
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Set<String> communitySet = new HashSet<>();
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if (organizationMap.containsKey(oTarget)) {
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communitySet.addAll(organizationMap.get(oTarget));
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}
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try{
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for (String oId : orgs) {
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if (organizationMap.containsKey(oId)) {
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communitySet.addAll(organizationMap.get(oId));
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.map(
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value -> {
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String rId = value.getResultId();
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Optional<List<String>> orgs = Optional.ofNullable(value.getMerges());
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String oTarget = value.getOrgId();
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Set<String> communitySet = new HashSet<>();
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if (organizationMap.containsKey(oTarget)) {
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communitySet.addAll(organizationMap.get(oTarget));
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}
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}
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}catch(Exception e){
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}
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if (communitySet.size() > 0){
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ResultCommunityList rcl = new ResultCommunityList();
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rcl.setResultId(rId);
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ArrayList<String> communityList = new ArrayList<>();
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communityList.addAll(communitySet);
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rcl.setCommunityList(communityList);
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return rcl;
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}
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return null;
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}, Encoders.bean(ResultCommunityList.class))
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.filter(r -> r!= null)
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.toJSON()
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.text(outputPath);
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if (orgs.isPresent())
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// try{
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for (String oId : orgs.get()) {
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if (organizationMap.containsKey(oId)) {
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communitySet.addAll(organizationMap.get(oId));
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}
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}
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// }catch(Exception e){
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//
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// }
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if (communitySet.size() > 0) {
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ResultCommunityList rcl = new ResultCommunityList();
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rcl.setResultId(rId);
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ArrayList<String> communityList = new ArrayList<>();
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communityList.addAll(communitySet);
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rcl.setCommunityList(communityList);
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return rcl;
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}
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return null;
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},
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Encoders.bean(ResultCommunityList.class))
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.filter(r -> r != null)
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.toJSON()
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.text(outputPath);
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}
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}
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@ -1,8 +1,13 @@
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package eu.dnetlib.dhp.resulttocommunityfromorganization;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.oaf.*;
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import java.util.*;
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import java.util.stream.Collectors;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.sql.Encoders;
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@ -10,25 +15,21 @@ import org.apache.spark.sql.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import java.util.*;
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import java.util.stream.Collectors;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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public class SparkResultToCommunityFromOrganizationJob2 {
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private static final Logger log = LoggerFactory.getLogger(SparkResultToCommunityFromOrganizationJob2.class);
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private static final Logger log =
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LoggerFactory.getLogger(SparkResultToCommunityFromOrganizationJob2.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils.toString(SparkResultToCommunityFromOrganizationJob2.class
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.getResourceAsStream("/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json"));
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String jsonConfiguration =
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IOUtils.toString(
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SparkResultToCommunityFromOrganizationJob2.class.getResourceAsStream(
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"/eu/dnetlib/dhp/resulttocommunityfromorganization/input_communitytoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -47,73 +48,79 @@ public class SparkResultToCommunityFromOrganizationJob2 {
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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final Boolean saveGraph = Optional
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.ofNullable(parser.get("saveGraph"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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final Boolean saveGraph =
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Optional.ofNullable(parser.get("saveGraph"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("saveGraph: {}", saveGraph);
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Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
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Class<? extends Result> resultClazz =
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(Class<? extends Result>) Class.forName(resultClassName);
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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runWithSparkHiveSession(conf, isSparkSessionManaged,
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runWithSparkHiveSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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if (isTest(parser)) {
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removeOutputDir(spark, outputPath);
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}
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execPropagation(spark, inputPath, outputPath, resultClazz, possibleupdatespath);
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});
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}
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private static <R extends Result> void execPropagation(SparkSession spark, String inputPath, String outputPath,
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Class<R> resultClazz, String possibleUpdatesPath) {
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org.apache.spark.sql.Dataset<ResultCommunityList> possibleUpdates = readResultCommunityList(spark, possibleUpdatesPath);
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private static <R extends Result> void execPropagation(
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SparkSession spark,
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String inputPath,
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String outputPath,
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Class<R> resultClazz,
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String possibleUpdatesPath) {
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org.apache.spark.sql.Dataset<ResultCommunityList> possibleUpdates =
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readResultCommunityList(spark, possibleUpdatesPath);
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org.apache.spark.sql.Dataset<R> result = readPathEntity(spark, inputPath, resultClazz);
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result
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.joinWith(possibleUpdates, result.col("id").equalTo(possibleUpdates.col("resultId")),
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result.joinWith(
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possibleUpdates,
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result.col("id").equalTo(possibleUpdates.col("resultId")),
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"left_outer")
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.map(value -> {
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R ret = value._1();
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Optional<ResultCommunityList> rcl = Optional.ofNullable(value._2());
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if(rcl.isPresent()){
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ArrayList<String> communitySet = rcl.get().getCommunityList();
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List<String> contextList = ret.getContext().stream().map(con -> con.getId()).collect(Collectors.toList());
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Result res = new Result();
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res.setId(ret.getId());
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List<Context> propagatedContexts = new ArrayList<>();
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for(String cId:communitySet){
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if(!contextList.contains(cId)){
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Context newContext = new Context();
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newContext.setId(cId);
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newContext.setDataInfo(Arrays.asList(getDataInfo(PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID, PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME)));
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propagatedContexts.add(newContext);
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.map(
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value -> {
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R ret = value._1();
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Optional<ResultCommunityList> rcl = Optional.ofNullable(value._2());
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if (rcl.isPresent()) {
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ArrayList<String> communitySet = rcl.get().getCommunityList();
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List<String> contextList =
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ret.getContext().stream()
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.map(con -> con.getId())
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.collect(Collectors.toList());
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Result res = new Result();
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res.setId(ret.getId());
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List<Context> propagatedContexts = new ArrayList<>();
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for (String cId : communitySet) {
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if (!contextList.contains(cId)) {
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Context newContext = new Context();
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newContext.setId(cId);
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newContext.setDataInfo(
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Arrays.asList(
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getDataInfo(
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PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_ID,
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PROPAGATION_RESULT_COMMUNITY_ORGANIZATION_CLASS_NAME)));
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propagatedContexts.add(newContext);
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}
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}
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res.setContext(propagatedContexts);
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ret.mergeFrom(res);
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}
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}
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res.setContext(propagatedContexts);
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ret.mergeFrom(res);
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}
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return ret;
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}, Encoders.bean(resultClazz))
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return ret;
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},
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Encoders.bean(resultClazz))
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.toJSON()
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression","gzip")
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.option("compression", "gzip")
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.text(outputPath);
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}
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private static org.apache.spark.sql.Dataset<ResultCommunityList> readResultCommunityList(SparkSession spark, String possibleUpdatesPath) {
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return spark
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.read()
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.textFile(possibleUpdatesPath)
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.map(value -> OBJECT_MAPPER.readValue(value, ResultCommunityList.class), Encoders.bean(ResultCommunityList.class));
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}
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}
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