modified the writing of the new relations. before: read old rels, add the new ones to them, write all the relations in new location. Now: first step of the wf copies the old relation i new location. If new relations are found, they are saved in the new location in append mode.
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@ -3,10 +3,9 @@ package eu.dnetlib.dhp.projecttoresult;
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import com.fasterxml.jackson.databind.ObjectMapper;
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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.schema.oaf.*;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.io.Text;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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@ -17,59 +16,65 @@ import org.apache.spark.sql.Row;
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import org.apache.spark.sql.SparkSession;
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import scala.Tuple2;
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import java.io.File;
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import java.util.*;
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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.Set;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.PropagationConstant.toPair;
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public class SparkResultToProjectThroughSemRelJob {
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public class SparkResultToProjectThroughSemRelJob2 {
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResultToProjectThroughSemRelJob.class.getResourceAsStream("/eu/dnetlib/dhp/projecttoresult/input_projecttoresult_parameters.json")));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils.toString(SparkResultToProjectThroughSemRelJob2.class
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.getResourceAsStream("/eu/dnetlib/dhp/projecttoresult/input_projecttoresult_parameters.json")));
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parser.parseArgument(args);
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parser.getObjectMap().keySet().stream().forEach(k -> System.out.println(k + " = " + parser.getObjectMap().get(k)));
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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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final SparkSession spark = SparkSession
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.builder()
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.appName(SparkResultToProjectThroughSemRelJob.class.getSimpleName())
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.appName(SparkResultToProjectThroughSemRelJob2.class.getSimpleName())
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.master(parser.get("master"))
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.config(conf)
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.enableHiveSupport()
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.getOrCreate();
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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final String inputPath = parser.get("sourcePath");
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final String outputPath = "/tmp/provision/propagation/projecttoresult";
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boolean writeUpdates = "true".equals(parser.get("writeUpdate"));
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boolean saveGraph = "true".equals(parser.get("saveGraph"));
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final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
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createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
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JavaRDD<Relation> all_relations = sc.textFile(inputPath + "/relation")
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.map(item -> new ObjectMapper().readValue(item, Relation.class));
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Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
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.map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
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relation.createOrReplaceTempView("relation");
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JavaRDD<Relation> relations = all_relations.filter(r -> !r.getDataInfo().getDeletedbyinference()).cache();
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String query = "Select source, target " +
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"from relation " +
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"where datainfo.deletedbyinference = false and relClass = '" + RELATION_RESULT_PROJECT_REL_CLASS + "'";
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JavaRDD<Relation> result_result = relations
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.filter(r -> allowedsemrel.contains(r.getRelClass()) && RELATION_RESULTRESULT_REL_TYPE.equals(r.getRelType()));
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org.apache.spark.sql.Dataset<Relation> resres_relation = spark.createDataset(result_result.rdd(),
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Encoders.bean(Relation.class));
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JavaRDD<Relation> result_project = relations
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.filter(r -> RELATION_RESULT_PROJECT_REL_CLASS.equals(r.getRelClass())
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&& RELATION_RESULTPROJECT_REL_TYPE.equals(r.getRelType()));
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org.apache.spark.sql.Dataset<Relation> resproj_relation = spark.createDataset(result_project.rdd(),
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Encoders.bean(Relation.class));
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Dataset<Row> resproj_relation = spark.sql(query);
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query = "Select source, target " +
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"from relation " +
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"where datainfo.deletedbyinference = false " + getConstraintList(" relClass = '", allowedsemrel );
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Dataset<Row> resres_relation = spark.sql(query);
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resres_relation.createOrReplaceTempView("resres_relation");
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resproj_relation.createOrReplaceTempView("resproj_relation");
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String query ="SELECT proj, collect_set(r1target) result_set " +
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query ="SELECT proj, collect_set(r1target) result_set " +
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"FROM (" +
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" SELECT r1.source as sourcer, r1.relclass as r1rel, r1.target as r1target, r2.target as proj " +
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" SELECT r1.source as source, r1.target as r1target, r2.target as proj " +
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" FROM resres_relation r1 " +
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" JOIN resproj_relation r2 " +
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" ON r1.source = r2.source " +
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@ -77,68 +82,63 @@ public class SparkResultToProjectThroughSemRelJob {
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"GROUP BY proj ";
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Dataset<Row> toaddrelations = spark.sql(query);
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query = "select target, collect_set(source) result_list from " +
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"resproj_relation " +
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"group by target";
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Dataset<Row> project_resultlist = spark.sql(query);
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JavaPairRDD<String, TypedRow> project_resultlist = relations
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.filter(r -> RELATION_PROJECT_RESULT_REL_CLASS.equals(r.getRelClass()))
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.map(r -> {
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TypedRow tp = new TypedRow();
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tp.setSourceId(r.getSource());
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tp.add(r.getTarget());
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return tp;
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}).mapToPair(toPair())
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.reduceByKey((a, b) -> {
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if (a == null) {
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return b;
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}
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if (b == null) {
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return a;
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}
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//if (writeUpdaes){
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toaddrelations.toJavaRDD().map(r->new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath + "/toupdaterelations");
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//}
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a.addAll(b.getAccumulator());
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return a;
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}).cache();
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JavaRDD<Relation> new_relations = toaddrelations.toJavaRDD().mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1)))
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.leftOuterJoin(project_resultlist)
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.flatMap(c -> {
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List<Object> toAddRel = new ArrayList<>();
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toAddRel.addAll(c._2()._1());
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if (c._2()._2().isPresent()) {
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Set<String> originalRels = c._2()._2().get().getAccumulator();
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for (String o : originalRels) {
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if (toAddRel.contains(o)) {
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toAddRel.remove(o);
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if(saveGraph){
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JavaRDD<Relation> new_relations = toaddrelations.toJavaRDD().mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1)))
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.leftOuterJoin(project_resultlist.toJavaRDD().mapToPair(pr -> new Tuple2<>(pr.getString(0), pr.getList(1))))
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.flatMap(c -> {
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List<Object> toAddRel = new ArrayList<>();
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toAddRel.addAll(c._2()._1());
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if (c._2()._2().isPresent()) {
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List<Object> originalRels = c._2()._2().get();
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for (Object o : originalRels) {
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if (toAddRel.contains(o)) {
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toAddRel.remove(o);
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}
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}
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}
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}
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List<Relation> relationList = new ArrayList<>();
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String projId = c._1();
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for (Object r : toAddRel) {
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String rId = (String) r;
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relationList.add(getRelation(rId, projId, RELATION_RESULT_PROJECT_REL_CLASS, RELATION_RESULTPROJECT_REL_TYPE,
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RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID,
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PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
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relationList.add(getRelation(projId, rId, RELATION_PROJECT_RESULT_REL_CLASS, RELATION_RESULTPROJECT_REL_TYPE,
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RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID,
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PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
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List<Relation> relationList = new ArrayList<>();
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String projId = c._1();
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for (Object r : toAddRel) {
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String rId = (String) r;
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relationList.add(getRelation(rId, projId, RELATION_RESULT_PROJECT_REL_CLASS, RELATION_RESULTPROJECT_REL_TYPE,
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RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID,
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PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
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relationList.add(getRelation(projId, rId, RELATION_PROJECT_RESULT_REL_CLASS, RELATION_RESULTPROJECT_REL_TYPE,
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RELATION_RESULTPROJECT_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_ID,
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PROPAGATION_RELATION_RESULT_PROJECT_SEM_REL_CLASS_NAME));
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}
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return relationList.iterator();
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}).cache();
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}
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if(relationList.size()==0){
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return null;
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}
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return relationList.iterator();
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}).filter(r -> !(r==null));
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toaddrelations.toJavaRDD().map(r->new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath + "/toupdaterelations");
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new_relations.map(r-> new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath + "/new_relations" );
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new_relations.map(r-> new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath + "/new_relations" );
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all_relations.union(new_relations)
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.map(r -> new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath + "/relation");
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sc.textFile(inputPath + "/relation")
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.map(item -> new ObjectMapper().readValue(item, Relation.class))
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.union(new_relations)
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.map(r -> new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath + "/relation");
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}
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//JavaPairRDD<String, TypedRow> result_result = getResultResultSemRel(allowedsemrel, relations);
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