forked from D-Net/dnet-hadoop
338 lines
16 KiB
Java
338 lines
16 KiB
Java
package eu.dnetlib.dhp.countrypropagation;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.PropagationConstant;
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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 net.sf.saxon.expr.ContextMappingFunction;
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import net.sf.saxon.expr.flwor.Tuple;
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import net.sf.saxon.om.Item;
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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.fs.Path;
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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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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.sql.*;
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import org.apache.spark.sql.Dataset;
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import org.codehaus.janino.Java;
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import scala.Tuple2;
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import javax.sql.DataSource;
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import java.beans.Encoder;
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import java.io.File;
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import java.io.IOException;
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import java.util.*;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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public class SparkCountryPropagationJob {
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCountryPropagationJob.class.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_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(SparkCountryPropagationJob.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 String inputPath = parser.get("sourcePath");
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final String outputPath = "/tmp/provision/propagation/countrytoresultfrominstitutionalrepositories";
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createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
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List<String> whitelist = Arrays.asList(parser.get("whitelist").split(";"));
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List<String> allowedtypes = Arrays.asList(parser.get("allowedtypes").split(";"));
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datasource(spark, whitelist, outputPath, inputPath);
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}
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private static void datasource(SparkSession spark, List<String> whitelist, String outputPath, String inputPath){
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String whitelisted = "";
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for (String i : whitelist){
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whitelisted += " OR id = '" + i + "'";
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}
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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Dataset<Datasource> datasource = spark.createDataset(sc.textFile(inputPath + "/datasource")
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.map(item -> new ObjectMapper().readValue(item, Datasource.class)).rdd(), Encoders.bean(Datasource.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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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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Dataset<eu.dnetlib.dhp.schema.oaf.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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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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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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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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datasource.createOrReplaceTempView("datasource");
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relation.createOrReplaceTempView("relation");
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organization.createOrReplaceTempView("organization");
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// String query = "SELECT source ds, target org, country.classid country " +
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// "FROM ( SELECT id " +
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// "FROM openaire.datasource " +
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// "WHERE datasourcetype.classid = 'pubsrepository::institutional' " +
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// "AND (datainfo.deletedbyinference = false " + whitelisted + ") ) d " +
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// "JOIN ( SELECT source, target " +
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// "FROM openaire.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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// "JOIN (SELECT id, country " +
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// "FROM openaire.organization " +
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// "WHERE datainfo.deletedbyinference = false ) o " +
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// "ON o.id = rel.target";
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String query = "SELECT source ds, target org, country.classid country " +
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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 " + whitelisted + ") ) 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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"JOIN (SELECT id, country " +
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"FROM organization " +
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"WHERE datainfo.deletedbyinference = false ) o " +
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"ON o.id = rel.target";
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Dataset<Row> rels = spark.sql(query);
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rels.createOrReplaceTempView("rels");
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software.createOrReplaceTempView("software");
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final JavaRDD<Row> toupdateresultsoftware = propagateOnResult(spark, "software");
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dataset.createOrReplaceTempView("dataset");
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final JavaRDD<Row> toupdateresultdataset = propagateOnResult(spark, "dataset");
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other.createOrReplaceTempView("other");
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final JavaRDD<Row> toupdateresultother = propagateOnResult(spark, "other");
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publication.createOrReplaceTempView("publication");
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final JavaRDD<Row> toupdateresultpublication = propagateOnResult(spark, "publication");
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writeUpdates(toupdateresultsoftware, toupdateresultdataset, toupdateresultother, toupdateresultpublication, outputPath);
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createUpdateForSoftwareDataset(toupdateresultsoftware, inputPath, spark)
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.map(s -> new ObjectMapper().writeValueAsString(s))
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.saveAsTextFile(outputPath + "/software");
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createUpdateForDatasetDataset(toupdateresultdataset,inputPath,spark)
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.map(d -> new ObjectMapper().writeValueAsString(d))
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.saveAsTextFile(outputPath + "/dataset");
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createUpdateForOtherDataset(toupdateresultother, inputPath, spark)
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.map(o -> new ObjectMapper().writeValueAsString(o))
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.saveAsTextFile(outputPath + "/otherresearchproduct");
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createUpdateForPublicationDataset(toupdateresultpublication, inputPath, spark)
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.map(p -> new ObjectMapper().writeValueAsString(p))
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.saveAsTextFile(outputPath + "/publication");
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}
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private static void writeUpdates(JavaRDD<Row> software, JavaRDD<Row> dataset, JavaRDD<Row> other , JavaRDD<Row> publication, String outputPath){
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createUpdateForResultDatasetWrite(software, outputPath, "update_software");
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createUpdateForResultDatasetWrite(dataset, outputPath, "update_dataset");
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createUpdateForResultDatasetWrite(other, outputPath, "update_other");
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createUpdateForResultDatasetWrite(publication, outputPath, "update_publication");
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}
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private static JavaRDD<OtherResearchProduct> createUpdateForOtherDataset(JavaRDD<Row> toupdateresult, String inputPath, SparkSession spark) {
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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return sc.textFile(inputPath + "/otherresearchproduct")
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.map(item -> new ObjectMapper().readValue(item, OtherResearchProduct.class))
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.mapToPair(s -> new Tuple2<>(s.getId(), s)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult))
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.map(c -> {
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OtherResearchProduct oaf = c._2()._1();
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List<Country> countryList = oaf.getCountry();
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if (c._2()._2().isPresent()) {
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HashSet<String> countries = new HashSet<>();
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for (Qualifier country : countryList) {
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countries.add(country.getClassid());
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}
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Result r = c._2()._2().get();
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for (Country country : r.getCountry()) {
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if (!countries.contains(country.getClassid())) {
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countryList.add(country);
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}
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}
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oaf.setCountry(countryList);
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}
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return oaf;
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});
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}
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private static JavaRDD<Publication> createUpdateForPublicationDataset(JavaRDD<Row> toupdateresult, String inputPath, SparkSession spark) {
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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return sc.textFile(inputPath + "/publication")
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.map(item -> new ObjectMapper().readValue(item, Publication.class))
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.mapToPair(s -> new Tuple2<>(s.getId(), s)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult))
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.map(c -> {
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Publication oaf = c._2()._1();
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List<Country> countryList = oaf.getCountry();
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if (c._2()._2().isPresent()) {
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HashSet<String> countries = new HashSet<>();
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for (Qualifier country : countryList) {
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countries.add(country.getClassid());
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}
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Result r = c._2()._2().get();
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for (Country country : r.getCountry()) {
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if (!countries.contains(country.getClassid())) {
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countryList.add(country);
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}
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}
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oaf.setCountry(countryList);
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}
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return oaf;
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});
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}
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private static JavaRDD<Software> createUpdateForSoftwareDataset(JavaRDD<Row> toupdateresult, String inputPath, SparkSession spark) {
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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return sc.textFile(inputPath + "/software")
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.map(item -> new ObjectMapper().readValue(item, Software.class))
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.mapToPair(s -> new Tuple2<>(s.getId(), s)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult))
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.map(c -> {
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Software oaf = c._2()._1();
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List<Country> countryList = oaf.getCountry();
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if (c._2()._2().isPresent()) {
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HashSet<String> countries = new HashSet<>();
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for (Qualifier country : countryList) {
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countries.add(country.getClassid());
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}
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Result r = c._2()._2().get();
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for (Country country : r.getCountry()) {
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if (!countries.contains(country.getClassid())) {
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countryList.add(country);
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}
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}
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oaf.setCountry(countryList);
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}
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return oaf;
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});
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}
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private static JavaRDD<eu.dnetlib.dhp.schema.oaf.Dataset> createUpdateForDatasetDataset(JavaRDD<Row> toupdateresult, String inputPath, SparkSession spark) {
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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return sc.textFile(inputPath + "/dataset")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Dataset.class))
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.mapToPair(d -> new Tuple2<>(d.getId(), d)).leftOuterJoin(getStringResultJavaPairRDD(toupdateresult))
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.map(c -> {
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eu.dnetlib.dhp.schema.oaf.Dataset oaf = c._2()._1();
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List<Country> countryList = oaf.getCountry();
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if (c._2()._2().isPresent()) {
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HashSet<String> countries = new HashSet<>();
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for (Qualifier country : countryList) {
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countries.add(country.getClassid());
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}
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Result r = c._2()._2().get();
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for (Country country : r.getCountry()) {
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if (!countries.contains(country.getClassid())) {
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countryList.add(country);
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}
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}
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oaf.setCountry(countryList);
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}
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return oaf;
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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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Dataset<Row> cfhb = spark.sql(query);
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cfhb.createOrReplaceTempView("cfhb");
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return countryPropagationAssoc(spark, "cfhb").toJavaRDD();
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}
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private static Dataset<Row> countryPropagationAssoc(SparkSession spark, String cfhbTable){
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String query = "SELECT id, collect_set(country) country "+
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"FROM ( SELECT id, country " +
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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 , country " +
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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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private static JavaPairRDD<String, Result> getStringResultJavaPairRDD(JavaRDD<Row> toupdateresult) {
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return toupdateresult.map(c -> {
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List<Country> countryList = new ArrayList<>();
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List<String> tmp = c.getList(1);
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for (String country : tmp) {
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countryList.add(getCountry(country));
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}
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Result r = new Result();
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r.setId(c.getString(0));
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r.setCountry(countryList);
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return r;
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}).mapToPair(r -> new Tuple2<>(r.getId(), r));
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}
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private static void createUpdateForResultDatasetWrite(JavaRDD<Row> toupdateresult, String outputPath, String type){
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toupdateresult.map(c -> {
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List<Country> countryList = new ArrayList<>();
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List<String> tmp = c.getList(1);
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for (String country : tmp) {
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countryList.add(getCountry(country));
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}
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Result r = new Result();
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r.setId(c.getString(0));
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r.setCountry(countryList);
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return r;
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}).map(r ->new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath+"/"+type);
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}
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}
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