[DUMP CSV] tested file to execute the dump of the relations with semantcis Cites from nodes belonging to a selected communities. It also dumps the relationships result_communities and prepare the ground for the dump of the results.
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@ -1,12 +1,15 @@
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package eu.dnetlib.dhp.oa.graph.dump.csv;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVCitation;
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import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVRELCommunityResult;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Optional;
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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.api.java.function.FilterFunction;
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@ -17,165 +20,204 @@ 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 eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVCitation;
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import eu.dnetlib.dhp.oa.graph.dump.csv.model.CSVRELCommunityResult;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.oaf.*;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import scala.Tuple2;
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import java.io.Serializable;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.List;
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import java.util.Optional;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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/**
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* @author miriam.baglioni
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* @Date 04/05/23
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*/
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//STEP 2
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public class SparkSelectResultsAndDumpRelations implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SparkSelectResultsAndDumpRelations.class);
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private static String RESULT_COMMUNITY_TABLE = "/result_community";
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private static String COMMUNITY_RESULT_IDS = "/communityResultIds";
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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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SparkSelectResultsAndDumpRelations.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/input_dump_csv_ste2.json"));
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private static final Logger log = LoggerFactory.getLogger(SparkSelectResultsAndDumpRelations.class);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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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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SparkSelectResultsAndDumpRelations.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/input_dump_csv_step1.json"));
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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final String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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Boolean isSparkSessionManaged = Optional
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.ofNullable(parser.get("isSparkSessionManaged"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final String inputPath = parser.get("isLoo");
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log.info("inputPath: {}", inputPath);
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final String workingPath = parser.get("workingPath");
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final String outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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List<String> communityList = null;
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Optional<String> communities = Optional.ofNullable(parser.get("communities"));
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if (communities.isPresent()) {
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communityList = Arrays.asList(communities.get().split(";"));
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}
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final String workingPath = parser.get("workingPath");
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SparkConf conf = new SparkConf();
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List<String> communityList = null;
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Optional<String> communities = Optional.ofNullable(parser.get("communities"));
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if(communities.isPresent()){
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communityList = Arrays.asList(communities.get().split(";"));
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}
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List<String> finalCommunityList = communityList;
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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Utils.removeOutputDir(spark, outputPath);
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run(spark, inputPath, outputPath, workingPath, finalCommunityList);
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SparkConf conf = new SparkConf();
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});
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List<String> finalCommunityList = communityList;
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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Utils.removeOutputDir(spark, outputPath );
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run(spark, inputPath, outputPath, workingPath, finalCommunityList);
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}
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});
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private static void run(SparkSession spark, String inputPath, String outputPath,
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String workingPath,
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List<String> communityList) {
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}
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private static <R extends Result> void run(SparkSession spark, String inputPath, String outputPath, String workingPath,
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List<String> communityList) {
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//select the result ids related to the set of communities considered
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writeCommunityRelatedIds(spark, inputPath + "/publication", Publication.class, communityList, workingPath + "/communityResultIds");
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writeCommunityRelatedIds(spark, inputPath + "/dataset", Dataset.class, communityList, workingPath + "/communityResultIds");
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writeCommunityRelatedIds(spark, inputPath + "/software", Software.class, communityList, workingPath + "/communityResultIds" );
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writeCommunityRelatedIds(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class, communityList, workingPath + "/communityResultIds");
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//write the relations result communities
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writeCommunityResultRelations(spark, inputPath + "/publication", Publication.class, communityList, workingPath + "/communityResultIds");
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writeCommunityResultRelations(spark, inputPath + "/dataset", Dataset.class, communityList, workingPath + "/communityResultIds");
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writeCommunityResultRelations(spark, inputPath + "/software", Software.class, communityList, workingPath + "/communityResultIds" );
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writeCommunityResultRelations(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class, communityList, workingPath + "/communityResultIds");
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//select the relations with semantics cites
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org.apache.spark.sql.Dataset<Relation> relations = Utils.readPath(spark, inputPath + "/relation", Relation.class)
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.filter((FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
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r.getRelClass().equals(ModelConstants.CITES));
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//select the results target of the selected relations having as source one of the results related to the communities
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org.apache.spark.sql.Dataset<String> resultIds = spark.read().textFile(outputPath + "/communityResultIds").distinct();
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resultIds.joinWith(relations, resultIds.col("value").equalTo(relations.col("source")), "left")
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.flatMap((FlatMapFunction<Tuple2<String, Relation>, String>) t2 -> {
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if(Optional.ofNullable(t2._2()).isPresent()){
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return Arrays.asList(t2._1(), t2._2().getTarget()).iterator();
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}else{
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return Arrays.asList(t2._1()).iterator();
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}
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}, Encoders.STRING())
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.distinct()
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression" , "gzip")
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.text(workingPath + "/resultIds");
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resultIds.joinWith(relations, resultIds.col("value").equalTo(relations.col("source")))
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.map((MapFunction<Tuple2<String, Relation>, CSVCitation>) t2 -> mapToCitation(t2._2()), Encoders.bean(CSVCitation.class) )
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Overwrite)
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.csv(outputPath + "/relation");
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// select the result ids related to the set of communities considered
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writeCommunityRelatedIds(
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spark, inputPath + "/publication", Publication.class, communityList, workingPath + COMMUNITY_RESULT_IDS);
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writeCommunityRelatedIds(
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spark, inputPath + "/dataset", Dataset.class, communityList, workingPath + COMMUNITY_RESULT_IDS);
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writeCommunityRelatedIds(
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spark, inputPath + "/software", Software.class, communityList, workingPath + COMMUNITY_RESULT_IDS);
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writeCommunityRelatedIds(
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spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class, communityList,
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workingPath + COMMUNITY_RESULT_IDS);
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}
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// write the relations result communities
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writeCommunityResultRelations(
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spark, inputPath + "/publication", Publication.class, communityList, outputPath + RESULT_COMMUNITY_TABLE);
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writeCommunityResultRelations(
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spark, inputPath + "/dataset", Dataset.class, communityList, outputPath + RESULT_COMMUNITY_TABLE);
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writeCommunityResultRelations(
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spark, inputPath + "/software", Software.class, communityList, outputPath + RESULT_COMMUNITY_TABLE);
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writeCommunityResultRelations(
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spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class, communityList,
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outputPath + RESULT_COMMUNITY_TABLE);
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private static CSVCitation mapToCitation(Relation relation) {
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CSVCitation ret = new CSVCitation();
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ret.setId(DHPUtils.md5(relation.getSource() + relation.getRelClass().toLowerCase() + relation.getTarget()));
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ret.setResult_id_cites(relation.getSource());
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ret.setResult_id_cited(relation.getTarget());
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return ret;
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}
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// select the relations with semantics cites
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org.apache.spark.sql.Dataset<Relation> relations = Utils
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.readPath(spark, inputPath + "/relation", Relation.class)
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.filter(
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(FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
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r.getRelClass().equals(ModelConstants.CITES));
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private static <R extends Result> void writeCommunityResultRelations(SparkSession spark, String inputPath, Class<R> clazz, List<String> communityList, String outputPath) {
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Utils
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.readPath(spark, inputPath , clazz)
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.filter((FilterFunction<R>) p -> !p.getDataInfo().getDeletedbyinference() &&
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!p.getDataInfo().getInvisible() )
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.flatMap((FlatMapFunction<R, CSVRELCommunityResult>) p-> {
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List<CSVRELCommunityResult> ret = new ArrayList<>();
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for(Context context : p.getContext()){
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String cId = context.getId().contains("::") ? context.getId().substring(0, context.getId().indexOf("::")) : context.getId();
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if (communityList.contains(cId)){
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CSVRELCommunityResult crc = new CSVRELCommunityResult();
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crc.setResult_id(p.getId());
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crc.setCommunity_id(DHPUtils.md5(cId));
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}
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}
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return ret.iterator();
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}, Encoders.bean(CSVRELCommunityResult.class) )
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.write()
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.option("compression","gzip")
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.mode(SaveMode.Append)
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.text(outputPath );
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}
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// select the results target of the selected relations having as source one of the results related to the
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// communities
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org.apache.spark.sql.Dataset<String> resultIds = spark
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.read()
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.textFile(workingPath + COMMUNITY_RESULT_IDS)
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.distinct();
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resultIds
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.joinWith(relations, resultIds.col("value").equalTo(relations.col("source")), "left")
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.flatMap((FlatMapFunction<Tuple2<String, Relation>, String>) t2 -> {
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if (Optional.ofNullable(t2._2()).isPresent()) {
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return Arrays.asList(t2._1(), t2._2().getTarget()).iterator();
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} else {
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return Arrays.asList(t2._1()).iterator();
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}
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}, Encoders.STRING())
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.distinct()
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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private static <R extends Result> void writeCommunityRelatedIds(SparkSession spark, String inputPath, Class<R> clazz, List<String> communityList, String outputPath) {
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Utils
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.readPath(spark, inputPath , clazz)
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.filter((FilterFunction<R>) p -> !p.getDataInfo().getDeletedbyinference() &&
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!p.getDataInfo().getInvisible() &&
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isRelatedToCommunities(p, communityList))
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.map((MapFunction<R, String>) p-> p.getId(), Encoders.STRING() )
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.write()
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.option("compression","gzip")
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.mode(SaveMode.Append)
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.text(outputPath );
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}
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.text(workingPath + "/resultIds");
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private static <R extends Result> boolean isRelatedToCommunities(R p, List<String> communityList) {
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return p.getContext().stream().anyMatch(c -> communityList.contains(c.getId()) ||
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(c.getId().contains("::") && communityList.contains(c.getId().substring(0, c.getId().indexOf("::")))));
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}
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resultIds
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.joinWith(relations, resultIds.col("value").equalTo(relations.col("source")))
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.map(
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(MapFunction<Tuple2<String, Relation>, CSVCitation>) t2 -> mapToCitation(t2._2()),
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Encoders.bean(CSVCitation.class))
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.write()
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.option("compression", "gzip")
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.option("header","true")
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.option("delimiter", Constants.SEP)
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.mode(SaveMode.Overwrite)
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.csv(outputPath + "/relation");
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}
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private static CSVCitation mapToCitation(Relation relation) {
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CSVCitation ret = new CSVCitation();
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ret.setId(DHPUtils.md5(relation.getSource() + relation.getRelClass().toLowerCase() + relation.getTarget()));
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ret.setResult_id_cites(relation.getSource());
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ret.setResult_id_cited(relation.getTarget());
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return ret;
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}
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private static <R extends Result> void writeCommunityResultRelations(SparkSession spark, String inputPath,
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Class<R> clazz, List<String> communityList, String outputPath) {
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Utils
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.readPath(spark, inputPath, clazz)
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.filter(
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(FilterFunction<R>) p -> !p.getDataInfo().getDeletedbyinference() &&
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!p.getDataInfo().getInvisible())
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.flatMap((FlatMapFunction<R, CSVRELCommunityResult>) p -> {
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List<CSVRELCommunityResult> ret = new ArrayList<>();
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for (String context :p.getContext().stream().map(Context::getId).distinct().collect(Collectors.toList())) {
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String cId = context.contains("::")
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? context.substring(0, context.indexOf("::"))
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: context;
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if (communityList.contains(cId)) {
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CSVRELCommunityResult crc = new CSVRELCommunityResult();
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crc.setResult_id(p.getId());
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crc.setCommunity_id(DHPUtils.md5(cId));
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ret.add(crc);
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}
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}
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return ret.iterator();
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}, Encoders.bean(CSVRELCommunityResult.class))
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Append)
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.option("header","true")
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.option("delimiter",Constants.SEP)
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.csv(outputPath);
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}
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private static <R extends Result> void writeCommunityRelatedIds(SparkSession spark, String inputPath,
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Class<R> clazz, List<String> communityList, String outputPath) {
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Utils
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.readPath(spark, inputPath, clazz)
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.filter(
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(FilterFunction<R>) p -> !p.getDataInfo().getDeletedbyinference() &&
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!p.getDataInfo().getInvisible() &&
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isRelatedToCommunities(p, communityList))
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.map((MapFunction<R, String>) Result::getId, Encoders.STRING())
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Append)
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.text(outputPath);
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}
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private static <R extends Result> boolean isRelatedToCommunities(R p, List<String> communityList) {
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return p
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.getContext()
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.stream()
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.anyMatch(
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c -> communityList.contains(c.getId()) ||
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(c.getId().contains("::")
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&& communityList.contains(c.getId().substring(0, c.getId().indexOf("::")))));
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}
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}
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