forked from D-Net/dnet-hadoop
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@ -14,9 +14,7 @@ import org.apache.spark.sql.SparkSession;
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import org.apache.hadoop.io.Text;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import java.io.File;
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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.*;
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import eu.dnetlib.dhp.schema.oaf.*;
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import scala.Tuple2;
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@ -50,7 +48,7 @@ public class SparkResultToOrganizationFromIstRepoJob {
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org.apache.spark.sql.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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org.apache.spark.sql.Dataset<Organization> organization = spark.createDataset(sc.textFile(inputPath + "/organziation")
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org.apache.spark.sql.Dataset<Organization> organization = spark.createDataset(sc.textFile(inputPath + "/organization")
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.map(item -> new ObjectMapper().readValue(item, Organization.class)).rdd(), Encoders.bean(Organization.class));
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datasource.createOrReplaceTempView("datasource");
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@ -102,8 +100,66 @@ public class SparkResultToOrganizationFromIstRepoJob {
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writeUpdates(toupdateresultsoftware, toupdateresultdataset, toupdateresultother, toupdateresultpublication, outputPath);
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query = "Select source resultId, collect_set(target) org_list " +
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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 +"' " +
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"group by source";
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JavaRDD<Row> result_orglist = spark.sql(query).toJavaRDD();
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JavaPairRDD<String, List<Object>> toupdateunion = toupdateresultdataset.mapToPair(d -> new Tuple2<>(d.getString(0), d.getList(1)))
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.union(toupdateresultother.mapToPair(o -> new Tuple2<>(o.getString(0), o.getList(1))))
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.union(toupdateresultpublication.mapToPair(p -> new Tuple2<>(p.getString(0), p.getList(1))))
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.union(toupdateresultsoftware.mapToPair(s -> new Tuple2<>(s.getString(0), s.getList(1))));
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JavaRDD<Relation> new_rels = getNewRels(result_orglist.mapToPair(r -> new Tuple2<>(r.getString(0), r.getList(1))),
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toupdateunion);
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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_rels)
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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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private static JavaRDD<Relation> getNewRels(JavaPairRDD<String, List<String>> relationOrgs, JavaPairRDD <String, List<Object>> newRels){
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return newRels
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.leftOuterJoin(relationOrgs)
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.flatMap(c -> {
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List<Object> toAddOrgs = new ArrayList<>();
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toAddOrgs.addAll(c._2()._1());
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if (c._2()._2().isPresent()) {
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Set<String> originalOrgs = new HashSet<>();
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originalOrgs.addAll(c._2()._2().get());
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for (Object oId : originalOrgs) {
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if (toAddOrgs.contains(oId)) {
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toAddOrgs.remove(oId);
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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 resId = c._1();
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for (Object org : toAddOrgs) {
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relationList.add(getRelation((String)org, resId, RELATION_ORGANIZATION_RESULT_REL_CLASS,
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RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
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relationList.add(getRelation(resId, (String)org, RELATION_RESULT_ORGANIZATION_REL_CLASS,
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RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
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}
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return relationList.iterator();
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});
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}
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private static void writeUpdates(JavaRDD<Row> toupdateresultsoftware, JavaRDD<Row> toupdateresultdataset, JavaRDD<Row> toupdateresultother, JavaRDD<Row> toupdateresultpublication, String outputPath) {
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createUpdateForRelationWrite(toupdateresultsoftware, outputPath, "update_software");
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createUpdateForRelationWrite(toupdateresultdataset, outputPath, "update_dataset");
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@ -160,3 +216,234 @@ public class SparkResultToOrganizationFromIstRepoJob {
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}
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}
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//package eu.dnetlib.dhp.resulttoorganizationfrominstrepo;
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//
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//import eu.dnetlib.dhp.TypedRow;
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//import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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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.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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//import org.apache.spark.api.java.JavaSparkContext;
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//import org.apache.spark.sql.Encoders;
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//import org.apache.spark.sql.Row;
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//import org.apache.spark.sql.SparkSession;
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//import org.apache.hadoop.io.Text;
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//import com.fasterxml.jackson.databind.ObjectMapper;
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//import java.io.File;
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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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//
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//import eu.dnetlib.dhp.schema.oaf.*;
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//import scala.Tuple2;
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//
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//import static eu.dnetlib.dhp.PropagationConstant.*;
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//
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//public class SparkResultToOrganizationFromIstRepoJob {
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// public static void main(String[] args) throws Exception {
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//
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// final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkResultToOrganizationFromIstRepoJob.class.getResourceAsStream("/eu/dnetlib/dhp/resulttoorganizationfrominstrepo/input_propagationresulaffiliationfrominstrepo_parameters.json")));
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// parser.parseArgument(args);
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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(SparkResultToOrganizationFromIstRepoJob.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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//
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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/resulttoorganizationfrominstitutionalrepositories";
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//
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// createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
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//
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// org.apache.spark.sql.Dataset<Datasource> datasource = spark.createDataset(sc.textFile(inputPath + "/datasource")
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// .map(item -> new ObjectMapper().readValue(item, Datasource.class))
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// .rdd(), Encoders.bean(Datasource.class));
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//
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// JavaRDD<Relation> relation_rdd_all = sc.textFile(inputPath + "/relation")
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// .map(item -> new ObjectMapper().readValue(item, Relation.class));
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// JavaRDD<Relation> relation_rdd = relation_rdd_all.filter(r -> !r.getDataInfo().getDeletedbyinference()).cache();
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//
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// org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(relation_rdd.rdd(), Encoders.bean(Relation.class));
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//
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// org.apache.spark.sql.Dataset<Organization> organization = spark.createDataset(sc.textFile(inputPath + "/organziation")
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// .map(item -> new ObjectMapper().readValue(item, Organization.class)).rdd(), Encoders.bean(Organization.class));
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//
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// datasource.createOrReplaceTempView("datasource");
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// relation.createOrReplaceTempView("relation");
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// organization.createOrReplaceTempView("organization");
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//
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// String query = "SELECT source ds, target org " +
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// "FROM ( SELECT id " +
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// "FROM datasource " +
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// "WHERE datasourcetype.classid = 'pubsrepository::institutional' " +
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// "AND datainfo.deletedbyinference = false ) d " +
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// "JOIN ( SELECT source, target " +
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// "FROM relation " +
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// "WHERE relclass = 'provides' " +
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// "AND datainfo.deletedbyinference = false ) rel " +
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// "ON d.id = rel.source ";
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//
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// org.apache.spark.sql.Dataset<Row> rels = spark.sql(query);
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// rels.createOrReplaceTempView("rels");
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//
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// org.apache.spark.sql.Dataset<Dataset> dataset = spark.createDataset(sc.textFile(inputPath + "/dataset")
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// .map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Dataset.class)).rdd(),
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// Encoders.bean(eu.dnetlib.dhp.schema.oaf.Dataset.class));
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//
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// org.apache.spark.sql.Dataset<OtherResearchProduct> other = spark.createDataset(sc.textFile(inputPath + "/otherresearchproduct")
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// .map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class)).rdd(),
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// Encoders.bean(eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class));
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//
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// org.apache.spark.sql.Dataset<Software> software = spark.createDataset(sc.textFile(inputPath + "/software")
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// .map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Software.class)).rdd(),
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// Encoders.bean(eu.dnetlib.dhp.schema.oaf.Software.class));
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//
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// org.apache.spark.sql.Dataset<Publication> publication = spark.createDataset(sc.textFile(inputPath + "/publication")
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// .map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Publication.class)).rdd(),
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// Encoders.bean(eu.dnetlib.dhp.schema.oaf.Publication.class));
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//
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//
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// software.createOrReplaceTempView("software");
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// final JavaRDD<Row> toupdateresultsoftware = propagateOnResult(spark, "software");
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//
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// dataset.createOrReplaceTempView("dataset");
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// final JavaRDD<Row> toupdateresultdataset = propagateOnResult(spark, "dataset");
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//
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// other.createOrReplaceTempView("other");
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// final JavaRDD<Row> toupdateresultother = propagateOnResult(spark, "other");
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//
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// publication.createOrReplaceTempView("publication");
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// final JavaRDD<Row> toupdateresultpublication = propagateOnResult(spark, "publication");
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//
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// writeUpdates(toupdateresultsoftware, toupdateresultdataset, toupdateresultother, toupdateresultpublication, outputPath);
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//
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// JavaPairRDD<String, TypedRow> relation_rdd_pair = relation_rdd
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// .filter(r -> RELATION_RESULT_ORGANIZATION_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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//
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// a.addAll(b.getAccumulator());
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// return a;
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// }).cache();
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//
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//
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// JavaRDD<Relation> new_rels = getNewRels(relation_rdd_pair,
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// toupdateresultother.mapToPair(s -> new Tuple2<>(s.getString(0), s.getList(1))))
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// .union(getNewRels(relation_rdd_pair,
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// toupdateresultsoftware.mapToPair(s -> new Tuple2<>(s.getString(0), s.getList(1)))))
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// .union(getNewRels(relation_rdd_pair,
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// toupdateresultdataset.mapToPair(s -> new Tuple2<>(s.getString(0), s.getList(1)))))
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// .union(getNewRels(relation_rdd_pair,
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// toupdateresultpublication.mapToPair(s -> new Tuple2<>(s.getString(0), s.getList(1)))));
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//
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//
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// relation_rdd_all.union(new_rels).map(r -> new ObjectMapper().writeValueAsString(r))
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// .saveAsTextFile(outputPath + "/relation");
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//
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// }
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//
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// private static JavaRDD<Relation> getNewRels(JavaPairRDD<String, TypedRow> relation_rdd_pair, JavaPairRDD <String, List<String>> newRels){
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// return newRels//.mapToPair(s -> new Tuple2<>(s.getString(0), s.getList(1)))
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// .leftOuterJoin(relation_rdd_pair)
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// .flatMap(c -> {
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// List<String> toAddOrgs = c._2()._1();
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// if (c._2()._2().isPresent()) {
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// Set<String> originalOrgs = c._2()._2().get().getAccumulator();
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// for (String oId : toAddOrgs) {
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// if (originalOrgs.contains(oId)) {
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// toAddOrgs.remove(oId);
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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 resId = c._1();
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// for (String org : toAddOrgs) {
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// relationList.add(getRelation(org, resId, RELATION_ORGANIZATION_RESULT_REL_CLASS,
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// RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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// PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
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// relationList.add(getRelation(resId, org, RELATION_RESULT_ORGANIZATION_REL_CLASS,
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// RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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// PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
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//
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// }
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// return relationList.iterator();
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// });
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//
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// }
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//
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// private static void writeUpdates(JavaRDD<Row> toupdateresultsoftware, JavaRDD<Row> toupdateresultdataset, JavaRDD<Row> toupdateresultother, JavaRDD<Row> toupdateresultpublication, String outputPath) {
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// createUpdateForRelationWrite(toupdateresultsoftware, outputPath, "update_software");
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// createUpdateForRelationWrite(toupdateresultdataset, outputPath, "update_dataset");
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// createUpdateForRelationWrite(toupdateresultother, outputPath, "update_other");
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// createUpdateForRelationWrite(toupdateresultpublication, outputPath, "update_publication");
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//
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// }
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//
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// private static void createUpdateForRelationWrite(JavaRDD<Row> toupdaterelation, String outputPath, String update_type) {
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// toupdaterelation.flatMap(s -> {
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// List<Relation> relationList = new ArrayList<>();
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// List<String> orgs = s.getList(1);
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// String resId = s.getString(0);
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// for (String org : orgs) {
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// relationList.add(getRelation(org, resId, RELATION_ORGANIZATION_RESULT_REL_CLASS,
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// RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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// PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
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// relationList.add(getRelation(resId, org, RELATION_RESULT_ORGANIZATION_REL_CLASS,
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// RELATION_RESULTORGANIZATION_REL_TYPE, RELATION_RESULTORGANIZATION_SUBREL_TYPE, PROPAGATION_DATA_INFO_TYPE,
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// PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_ID, PROPAGATION_RELATION_RESULT_ORGANIZATION_INST_REPO_CLASS_NAME));
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//
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// }
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// return relationList.iterator();
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// }).map(s -> new ObjectMapper().writeValueAsString(s)).saveAsTextFile(outputPath + "/" + update_type);
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// }
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//
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// private static JavaRDD<Row> propagateOnResult(SparkSession spark, String table) {
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// String query;
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// query = "SELECT id, inst.collectedfrom.key cf , inst.hostedby.key hb " +
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// "FROM ( SELECT id, instance " +
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// "FROM " + table +
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// " WHERE datainfo.deletedbyinference = false) ds " +
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// "LATERAL VIEW EXPLODE(instance) i AS inst";
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// org.apache.spark.sql.Dataset<Row> cfhb = spark.sql(query);
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// cfhb.createOrReplaceTempView("cfhb");
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//
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// return organizationPropagationAssoc(spark, "cfhb").toJavaRDD();
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//
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// }
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//
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// private static org.apache.spark.sql.Dataset<Row> organizationPropagationAssoc(SparkSession spark, String cfhbTable){
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// String query = "SELECT id, collect_set(org) org "+
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// "FROM ( SELECT id, org " +
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// "FROM rels " +
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// "JOIN " + cfhbTable +
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// " ON cf = ds " +
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// "UNION ALL " +
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// "SELECT id , org " +
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// "FROM rels " +
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// "JOIN " + cfhbTable +
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// " ON hb = ds ) tmp " +
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// "GROUP BY id";
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// return spark.sql(query);
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// }
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//
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//}
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