146 lines
4.8 KiB
Java
146 lines
4.8 KiB
Java
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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 java.util.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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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 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.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import scala.Tuple2;
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public class PrepareResultCommunitySet {
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private static final Logger log = LoggerFactory.getLogger(PrepareResultCommunitySet.class);
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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PrepareResultCommunitySet.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/resulttocommunityfromorganization/input_preparecommunitytoresult_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(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()
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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(
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conf,
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isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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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(
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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 = readPath(spark, inputPath, Relation.class);
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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 lower(relClass) = '"
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+ ModelConstants.HAS_AUTHOR_INSTITUTION.toLowerCase()
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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 lower(relClass) = '"
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+ ModelConstants.MERGES.toLowerCase()
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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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Dataset<ResultOrganizations> result_organizationset = spark
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.sql(query)
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.as(Encoders.bean(ResultOrganizations.class));
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result_organizationset
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.map(mapResultCommunityFn(organizationMap), Encoders.bean(ResultCommunityList.class))
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.filter(Objects::nonNull)
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.toJavaRDD()
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.mapToPair(value -> new Tuple2<>(value.getResultId(), value))
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.reduceByKey((a, b) -> {
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ArrayList<String> cl = a.getCommunityList();
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b.getCommunityList().stream().forEach(s -> {
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if (!cl.contains(s)) {
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cl.add(s);
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}
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});
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a.setCommunityList(cl);
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return a;
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})
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.map(value -> OBJECT_MAPPER.writeValueAsString(value._2()))
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.saveAsTextFile(outputPath, GzipCodec.class);
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// .write()
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// .mode(SaveMode.Overwrite)
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// .option("compression", "gzip")
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// .json(outputPath);
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}
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private static MapFunction<ResultOrganizations, ResultCommunityList> mapResultCommunityFn(
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OrganizationMap organizationMap) {
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return (MapFunction<ResultOrganizations, ResultCommunityList>) 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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if (orgs.isPresent())
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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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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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}
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}
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