forked from D-Net/dnet-hadoop
preparation phase for the propagation of community to result from organization
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@ -1,4 +1,120 @@
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package eu.dnetlib.dhp.resulttocommunityfromorganization;
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package eu.dnetlib.dhp.resulttocommunityfromorganization;
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public class PrepareInfo {
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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.TypedRow;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.orcidtoresultfromsemrel.PrepareResultOrcidAssociationStep1;
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import eu.dnetlib.dhp.orcidtoresultfromsemrel.SparkOrcidToResultFromSemRelJob3;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.Result;
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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.api.java.JavaRDD;
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import org.apache.spark.api.java.function.MapFunction;
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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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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_communitytoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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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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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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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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});
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}
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private static void prepareInfo(SparkSession spark, String inputPath, String outputPath, 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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org.apache.spark.sql.Dataset<ResultOrganizations> result_organizationset = spark.sql(query)
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.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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}
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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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}
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}
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}
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