master #11
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@ -14,14 +14,13 @@ import org.apache.spark.sql.SaveMode;
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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.PropagationConstant.createOutputDirs;
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import static eu.dnetlib.dhp.PropagationConstant.getConstraintList;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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/**
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* For the association of the country to the datasource
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@ -38,53 +37,46 @@ public class PrepareResultCountryAssociation {
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils.toString(PrepareResultCountryAssociation.class
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.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json"));
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.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_prepare_dc_assoc.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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parser.parseArgument(args);
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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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String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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String graphTableClassName = parser.get("graphTableClassName");
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log.info("graphTableClassName: {}", graphTableClassName);
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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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runWithSparkSession(conf, isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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joinRelationEntity(spark, inputRelationsPath, inputEntityPath, entityClazz, outputPath);
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});
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final SparkSession spark = SparkSession
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.builder()
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.appName(PrepareResultCountryAssociation.class.getSimpleName())
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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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//todo add link to working dir
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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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prepareDatasourceCountryAssociation(spark,
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Arrays.asList(parser.get("whitelist").split(";")),
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Arrays.asList(parser.get("allowedtypes").split(";")),
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inputPath,
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outputPath);
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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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}
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private static void prepareDatasourceCountryAssociation(SparkSession spark,
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List<String> whitelist,
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List<String> allowedtypes,
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String inputPath,
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String outputPath) {
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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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@ -93,13 +85,13 @@ public class PrepareResultCountryAssociation {
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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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.map(item -> OBJECT_MAPPER.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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.map(item -> OBJECT_MAPPER.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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.map(item -> OBJECT_MAPPER.readValue(item, Organization.class)).rdd(), Encoders.bean(Organization.class));
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datasource.createOrReplaceTempView("datasource");
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relation.createOrReplaceTempView("relation");
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@ -107,18 +99,18 @@ public class PrepareResultCountryAssociation {
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String query = "SELECT source ds, country.classid country " +
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"FROM ( SELECT id " +
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"FROM datasource " +
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"WHERE (datainfo.deletedbyinference = false " + whitelisted + ") " +
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getConstraintList("datasourcetype.classid = '", allowedtypes) + ") d " +
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" FROM datasource " +
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" WHERE (datainfo.deletedbyinference = false " + whitelisted + ") " +
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getConstraintList("datasourcetype.classid = '", allowedtypes) + ") 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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" 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 " +
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"AND length(country.classid)>0) o " +
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" FROM organization " +
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" WHERE datainfo.deletedbyinference = false " +
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" AND length(country.classid)>0) o " +
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"ON o.id = rel.target";
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spark.sql(query)
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@ -129,4 +121,6 @@ public class PrepareResultCountryAssociation {
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}
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}
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@ -4,21 +4,17 @@ import com.fasterxml.jackson.databind.ObjectMapper;
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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 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.api.java.function.MapFunction;
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import org.apache.spark.broadcast.Broadcast;
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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.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 scala.Tuple2;
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import java.util.ArrayList;
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import java.util.Arrays;
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import java.util.HashSet;
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import java.util.List;
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import java.util.*;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import org.slf4j.Logger;
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@ -32,8 +28,25 @@ public class SparkCountryPropagationJob2 {
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkCountryPropagationJob2.class.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json")));
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String jsonConfiguration = IOUtils.toString(SparkCountryPropagationJob2.class
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.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_countrypropagation_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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parser.parseArgument(args);
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String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String outputPath = "/tmp/provision/propagation/countrytoresultfrominstitutionalrepositories";
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final String datasourcecountrypath = outputPath + "/prepared_datasource_country";
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final String resultClassName = parser.get("resultClazz");
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final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".")+1);
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Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
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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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@ -44,242 +57,135 @@ public class SparkCountryPropagationJob2 {
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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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boolean writeUpdates = TRUE.equals(parser.get("writeUpdate"));
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boolean saveGraph = TRUE.equals(parser.get("saveGraph"));
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final boolean writeUpdates = TRUE.equals(parser.get("writeUpdate"));
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final boolean saveGraph = TRUE.equals(parser.get("saveGraph"));
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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//Load parque file with preprocessed association datasource - country
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Dataset<DatasourceCountry> datasourcecountryassoc = readAssocDatasourceCountry(spark, datasourcecountrypath);
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//broadcasting the result of the preparation step
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Broadcast<Dataset<DatasourceCountry>> broadcast_datasourcecountryassoc = sc.broadcast(datasourcecountryassoc);
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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, OtherResearchProduct.class)).rdd(),
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Encoders.bean(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, Software.class)).rdd(),
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Encoders.bean(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, Publication.class)).rdd(),
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Encoders.bean(Publication.class));
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//todo broadcast
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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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Dataset<Row> potentialUpdates = getPotentialResultToUpdate(spark, inputPath, resultClazz, broadcast_datasourcecountryassoc);
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if(writeUpdates){
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writeUpdates(toupdateresultsoftware, toupdateresultdataset, toupdateresultother, toupdateresultpublication, outputPath);
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writeUpdates(potentialUpdates.toJavaRDD(), outputPath + "/update_" + resultType);
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}
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if(saveGraph){
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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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updateResultTable(spark, potentialUpdates, inputPath, resultClazz, outputPath + "/" + resultType);
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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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}
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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 <R extends Result> void updateResultTable(SparkSession spark, Dataset<Row> potentialUpdates,
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String inputPath,
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Class<R> resultClazz,
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String outputPath) {
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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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Dataset<R> result = readPathEntity(spark, inputPath, resultClazz);
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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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Dataset<Tuple2<String, R>> result_pair = result
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.map(r -> new Tuple2<>(r.getId(), r),
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Encoders.tuple(Encoders.STRING(), Encoders.bean(resultClazz)));
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Dataset<Tuple2<String, List>> potential_update_pair = potentialUpdates.map(pu -> new Tuple2<>(pu.getString(0), pu.getList(1)),
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Encoders.tuple(Encoders.STRING(), Encoders.bean(List.class)));
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Dataset<R> new_table = result_pair
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.joinWith(potential_update_pair, result_pair.col("_1").equalTo(potential_update_pair.col("_1")), "left")
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.map((MapFunction<Tuple2<Tuple2<String, R>, Tuple2<String, List>>, R>) value -> {
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R r = value._1()._2();
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Optional<List<Object>> potentialNewCountries = Optional.ofNullable(value._2()).map(Tuple2::_2);
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if (potentialNewCountries != null) {
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HashSet<String> countries = new HashSet<>();
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for (Qualifier country : countryList) {
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for (Qualifier country : r.getCountry()) {
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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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for (Object country : potentialNewCountries.get()) {
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if (!countries.contains(country)) {
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r.getCountry().add(getCountry((String) 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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return r;
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}, Encoders.bean(resultClazz));
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log.info("Saving graph table to path: {}", outputPath);
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result
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.toJSON()
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.write()
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.option("compression", "gzip")
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.text(outputPath);
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}
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private static <R extends Result> Dataset<Row> getPotentialResultToUpdate(SparkSession spark, String inputPath,
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Class<R> resultClazz,
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Broadcast<Dataset<DatasourceCountry>> broadcast_datasourcecountryassoc) {
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Dataset<R> result = readPathEntity(spark, inputPath, resultClazz);
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result.createOrReplaceTempView("result");
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createCfHbforresult(spark);
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return countryPropagationAssoc(spark, broadcast_datasourcecountryassoc);
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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 -> {
|
||||
eu.dnetlib.dhp.schema.oaf.Dataset oaf = c._2()._1();
|
||||
List<Country> countryList = oaf.getCountry();
|
||||
if (c._2()._2().isPresent()) {
|
||||
HashSet<String> countries = new HashSet<>();
|
||||
for (Qualifier country : countryList) {
|
||||
countries.add(country.getClassid());
|
||||
}
|
||||
Result r = c._2()._2().get();
|
||||
for (Country country : r.getCountry()) {
|
||||
if (!countries.contains(country.getClassid())) {
|
||||
countryList.add(country);
|
||||
}
|
||||
}
|
||||
oaf.setCountry(countryList);
|
||||
}
|
||||
return oaf;
|
||||
});
|
||||
}
|
||||
|
||||
private static JavaRDD<Row> propagateOnResult(SparkSession spark, String result_type) {
|
||||
private static void createCfHbforresult(SparkSession spark) {
|
||||
String query;
|
||||
query = "SELECT id, inst.collectedfrom.key cf , inst.hostedby.key hb " +
|
||||
"FROM ( SELECT id, instance " +
|
||||
"FROM " + result_type +
|
||||
"FROM result " +
|
||||
" WHERE datainfo.deletedbyinference = false) ds " +
|
||||
"LATERAL VIEW EXPLODE(instance) i AS inst";
|
||||
Dataset<Row> cfhb = spark.sql(query);
|
||||
cfhb.createOrReplaceTempView("cfhb");
|
||||
|
||||
return countryPropagationAssoc(spark, "cfhb").toJavaRDD();
|
||||
|
||||
}
|
||||
|
||||
private static Dataset<Row> countryPropagationAssoc(SparkSession spark, String cfhbTable){
|
||||
|
||||
private static Dataset<Row> countryPropagationAssoc(SparkSession spark,
|
||||
Broadcast<Dataset<DatasourceCountry>> broadcast_datasourcecountryassoc){
|
||||
Dataset<DatasourceCountry> datasource_country = broadcast_datasourcecountryassoc.value();
|
||||
datasource_country.createOrReplaceTempView("datasource_country");
|
||||
|
||||
String query = "SELECT id, collect_set(country) country "+
|
||||
"FROM ( SELECT id, country " +
|
||||
"FROM rels " +
|
||||
"JOIN " + cfhbTable +
|
||||
"JOIN cfhb " +
|
||||
" ON cf = ds " +
|
||||
"UNION ALL " +
|
||||
"SELECT id , country " +
|
||||
"FROM rels " +
|
||||
"JOIN " + cfhbTable +
|
||||
"JOIN cfhb " +
|
||||
" ON hb = ds ) tmp " +
|
||||
"GROUP BY id";
|
||||
return spark.sql(query);
|
||||
}
|
||||
|
||||
private static JavaPairRDD<String, Result> getStringResultJavaPairRDD(JavaRDD<Row> toupdateresult) {
|
||||
return toupdateresult.map(c -> {
|
||||
List<Country> countryList = new ArrayList<>();
|
||||
List<String> tmp = c.getList(1);
|
||||
for (String country : tmp) {
|
||||
countryList.add(getCountry(country));
|
||||
}
|
||||
Result r = new Result();
|
||||
r.setId(c.getString(0));
|
||||
r.setCountry(countryList);
|
||||
return r;
|
||||
}).mapToPair(r -> new Tuple2<>(r.getId(), r));
|
||||
private static <R extends Result> Dataset<R> readPathEntity(SparkSession spark, String inputEntityPath, Class<R> resultClazz) {
|
||||
|
||||
log.info("Reading Graph table from: {}", inputEntityPath);
|
||||
return spark
|
||||
.read()
|
||||
.textFile(inputEntityPath)
|
||||
.map((MapFunction<String, R>) value -> OBJECT_MAPPER.readValue(value, resultClazz), Encoders.bean(resultClazz));
|
||||
}
|
||||
|
||||
private static void createUpdateForResultDatasetWrite(JavaRDD<Row> toupdateresult, String outputPath, String type){
|
||||
toupdateresult.map(c -> {
|
||||
List<Country> countryList = new ArrayList<>();
|
||||
List<String> tmp = c.getList(1);
|
||||
for (String country : tmp) {
|
||||
countryList.add(getCountry(country));
|
||||
}
|
||||
Result r = new Result();
|
||||
r.setId(c.getString(0));
|
||||
r.setCountry(countryList);
|
||||
return r;
|
||||
private static Dataset<DatasourceCountry> readAssocDatasourceCountry(SparkSession spark, String relationPath) {
|
||||
return spark.read()
|
||||
.load(relationPath)
|
||||
.as(Encoders.bean(DatasourceCountry.class));
|
||||
}
|
||||
|
||||
}).map(r ->new ObjectMapper().writeValueAsString(r))
|
||||
.saveAsTextFile(outputPath+"/"+type);
|
||||
private static void writeUpdates(JavaRDD<Row> potentialUpdates, String outputPath){
|
||||
potentialUpdates.map(u -> OBJECT_MAPPER.writeValueAsString(u))
|
||||
.saveAsTextFile(outputPath);
|
||||
}
|
||||
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue