master #11
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@ -1,47 +1,43 @@
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package eu.dnetlib.dhp.countrypropagation;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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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 java.util.Arrays;
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import java.util.List;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaSparkContext;
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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.SparkSession;
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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 org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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/**
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* For the association of the country to the datasource
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* The association is computed only for datasource of specific type or having whitelisted ids
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* The country is registered in the Organization associated to the Datasource, so the
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* relation provides between Datasource and Organization is exploited to get the country for the datasource
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* For the association of the country to the datasource The association is computed only for
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* datasource of specific type or having whitelisted ids The country is registered in the
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* Organization associated to the Datasource, so the relation provides between Datasource and
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* Organization is exploited to get the country for the datasource
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*/
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public class PrepareDatasourceCountryAssociation {
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private static final Logger log = LoggerFactory.getLogger(PrepareDatasourceCountryAssociation.class);
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private static final Logger log =
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LoggerFactory.getLogger(PrepareDatasourceCountryAssociation.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils.toString(PrepareDatasourceCountryAssociation.class
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.getResourceAsStream("/eu/dnetlib/dhp/countrypropagation/input_prepareassoc_parameters.json"));
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String jsonConfiguration =
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IOUtils.toString(
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PrepareDatasourceCountryAssociation.class.getResourceAsStream(
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"/eu/dnetlib/dhp/countrypropagation/input_prepareassoc_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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jsonConfiguration);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -57,73 +53,83 @@ public class PrepareDatasourceCountryAssociation {
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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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runWithSparkHiveSession(conf, isSparkSessionManaged,
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runWithSparkHiveSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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removeOutputDir(spark, outputPath);
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prepareDatasourceCountryAssociation(spark,
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prepareDatasourceCountryAssociation(
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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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});
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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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private static void prepareDatasourceCountryAssociation(
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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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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 =
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spark.createDataset(
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sc.textFile(inputPath + "/datasource")
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.map(item -> OBJECT_MAPPER.readValue(item, Datasource.class))
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.rdd(),
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Encoders.bean(Datasource.class));
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Dataset<Datasource> datasource = spark.createDataset(sc.textFile(inputPath + "/datasource")
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.map(item -> OBJECT_MAPPER.readValue(item, Datasource.class)).rdd(), Encoders.bean(Datasource.class));
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Dataset<Relation> relation =
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spark.createDataset(
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sc.textFile(inputPath + "/relation")
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.map(item -> OBJECT_MAPPER.readValue(item, Relation.class))
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.rdd(),
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Encoders.bean(Relation.class));
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Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
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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 -> OBJECT_MAPPER.readValue(item, Organization.class)).rdd(), Encoders.bean(Organization.class));
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Dataset<Organization> organization =
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spark.createDataset(
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sc.textFile(inputPath + "/organization")
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.map(item -> OBJECT_MAPPER.readValue(item, Organization.class))
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.rdd(),
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Encoders.bean(Organization.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 dataSourceId, named_struct('classid', country.classid, 'classname', country.classname) 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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"JOIN ( SELECT source, target " +
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" FROM relation " +
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" WHERE relclass = '" + RELATION_DATASOURCE_ORGANIZATION_REL_CLASS + "' " +
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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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"ON o.id = rel.target";
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String query =
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"SELECT source dataSourceId, named_struct('classid', country.classid, 'classname', country.classname) country "
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+ "FROM ( SELECT id "
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+ " FROM datasource "
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+ " WHERE (datainfo.deletedbyinference = false "
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+ whitelisted
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+ ") "
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+ getConstraintList("datasourcetype.classid = '", allowedtypes)
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+ ") d "
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+ "JOIN ( SELECT source, target "
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+ " FROM relation "
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+ " WHERE relclass = '"
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+ RELATION_DATASOURCE_ORGANIZATION_REL_CLASS
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+ "' "
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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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+ "ON o.id = rel.target";
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spark.sql(query)
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.as(Encoders.bean(DatasourceCountry.class))
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.toJavaRDD()
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.map(c -> OBJECT_MAPPER.writeValueAsString(c))
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.saveAsTextFile(outputPath, GzipCodec.class);
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}
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}
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@ -1,28 +1,22 @@
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package eu.dnetlib.dhp.countrypropagation;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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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 java.util.*;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.fs.FileSystem;
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import org.apache.hadoop.io.compress.CompressionCodec;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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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 scala.Tuple2;
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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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import org.slf4j.LoggerFactory;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession;
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import scala.Tuple2;
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public class SparkCountryPropagationJob2 {
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@ -30,14 +24,14 @@ public class SparkCountryPropagationJob2 {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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public static void main(String[] args) throws Exception {
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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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String jsonConfiguration =
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IOUtils.toString(
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SparkCountryPropagationJob2.class.getResourceAsStream(
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"/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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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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@ -56,182 +50,214 @@ public class SparkCountryPropagationJob2 {
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final String resultClassName = parser.get("resultTableName");
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log.info("resultTableName: {}", resultClassName);
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final String resultType = resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
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final String resultType =
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resultClassName.substring(resultClassName.lastIndexOf(".") + 1).toLowerCase();
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log.info("resultType: {}", resultType);
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final Boolean writeUpdates = Optional
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.ofNullable(parser.get("writeUpdate"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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final Boolean writeUpdates =
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Optional.ofNullable(parser.get("writeUpdate"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("writeUpdate: {}", writeUpdates);
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final Boolean saveGraph = Optional
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.ofNullable(parser.get("saveGraph"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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final Boolean saveGraph =
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Optional.ofNullable(parser.get("saveGraph"))
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.map(Boolean::valueOf)
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.orElse(Boolean.TRUE);
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log.info("saveGraph: {}", saveGraph);
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Class<? extends Result> resultClazz = (Class<? extends Result>) Class.forName(resultClassName);
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Class<? extends Result> resultClazz =
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(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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runWithSparkHiveSession(conf, isSparkSessionManaged,
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runWithSparkHiveSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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//createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
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// createOutputDirs(outputPath,
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// FileSystem.get(spark.sparkContext().hadoopConfiguration()));
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removeOutputDir(spark, outputPath);
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execPropagation(spark, datasourcecountrypath, inputPath, outputPath, resultClazz, resultType,
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writeUpdates, saveGraph);
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execPropagation(
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spark,
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datasourcecountrypath,
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inputPath,
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outputPath,
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resultClazz,
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resultType,
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writeUpdates,
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saveGraph);
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});
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}
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private static <R extends Result> void execPropagation(SparkSession spark, String datasourcecountrypath,
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String inputPath, String outputPath, Class<R> resultClazz, String resultType,
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boolean writeUpdates, boolean saveGraph){
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private static <R extends Result> void execPropagation(
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SparkSession spark,
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String datasourcecountrypath,
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String inputPath,
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String outputPath,
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Class<R> resultClazz,
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String resultType,
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boolean writeUpdates,
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boolean 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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// Load parque file with preprocessed association datasource - country
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Dataset<DatasourceCountry> datasourcecountryassoc =
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readAssocDatasourceCountry(spark, datasourcecountrypath);
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// broadcasting the result of the preparation step
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Broadcast<Dataset<DatasourceCountry>> broadcast_datasourcecountryassoc =
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sc.broadcast(datasourcecountryassoc);
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Dataset<ResultCountrySet> potentialUpdates = getPotentialResultToUpdate(spark, inputPath, resultClazz,
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broadcast_datasourcecountryassoc).as(Encoders.bean(ResultCountrySet.class));
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Dataset<ResultCountrySet> potentialUpdates =
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getPotentialResultToUpdate(
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spark, inputPath, resultClazz, broadcast_datasourcecountryassoc)
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.as(Encoders.bean(ResultCountrySet.class));
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if(writeUpdates){
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if (writeUpdates) {
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writeUpdates(potentialUpdates, outputPath + "/update_" + resultType);
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}
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if(saveGraph){
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if (saveGraph) {
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updateResultTable(spark, potentialUpdates, inputPath, resultClazz, outputPath);
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}
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}
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private static <R extends Result> void updateResultTable(SparkSession spark, Dataset<ResultCountrySet> 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 <R extends Result> void updateResultTable(
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SparkSession spark,
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Dataset<ResultCountrySet> potentialUpdates,
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String inputPath,
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Class<R> resultClazz,
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String outputPath) {
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log.info("Reading Graph table from: {}", inputPath);
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Dataset<R> result = readPathEntity(spark, inputPath, resultClazz);
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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, R>> result_pair =
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result.map(
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r -> new Tuple2<>(r.getId(), r),
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Encoders.tuple(Encoders.STRING(), Encoders.bean(resultClazz)));
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// Dataset<Tuple2<String, ResultCountrySet>> potential_update_pair = potentialUpdates.map(pu -> new Tuple2<>(pu.getResultId(),
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// pu),
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// Encoders.tuple(Encoders.STRING(), Encoders.bean(ResultCountrySet.class)));
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// Dataset<Tuple2<String, ResultCountrySet>> potential_update_pair =
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// potentialUpdates.map(pu -> new Tuple2<>(pu.getResultId(),
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// pu),
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// Encoders.tuple(Encoders.STRING(), Encoders.bean(ResultCountrySet.class)));
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Dataset<R> new_table = result_pair
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.joinWith(potentialUpdates, result_pair.col("_1").equalTo(potentialUpdates.col("resultId")), "left_outer")
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.map((MapFunction<Tuple2<Tuple2<String, R>, ResultCountrySet>, R>) value -> {
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R r = value._1()._2();
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Optional<ResultCountrySet> potentialNewCountries = Optional.ofNullable(value._2());
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if (potentialNewCountries.isPresent()) {
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HashSet<String> countries = new HashSet<>();
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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 res = new Result();
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res.setId(r.getId());
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List<Country> countryList = new ArrayList<>();
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for (CountrySbs country : potentialNewCountries.get().getCountrySet()) {
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if (!countries.contains(country.getClassid())) {
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countryList.add(getCountry(country.getClassid(), country.getClassname()));
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}
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}
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res.setCountry(countryList);
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r.mergeFrom(res);
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}
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return r;
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}, Encoders.bean(resultClazz));
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Dataset<R> new_table =
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result_pair
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.joinWith(
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potentialUpdates,
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result_pair.col("_1").equalTo(potentialUpdates.col("resultId")),
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"left_outer")
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.map(
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(MapFunction<Tuple2<Tuple2<String, R>, ResultCountrySet>, R>)
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value -> {
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R r = value._1()._2();
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Optional<ResultCountrySet> potentialNewCountries =
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Optional.ofNullable(value._2());
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if (potentialNewCountries.isPresent()) {
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HashSet<String> countries = new HashSet<>();
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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 res = new Result();
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res.setId(r.getId());
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List<Country> countryList = new ArrayList<>();
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for (CountrySbs country :
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potentialNewCountries
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.get()
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.getCountrySet()) {
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if (!countries.contains(country.getClassid())) {
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countryList.add(
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getCountry(
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country.getClassid(),
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country.getClassname()));
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}
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}
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res.setCountry(countryList);
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r.mergeFrom(res);
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}
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return r;
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},
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Encoders.bean(resultClazz));
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log.info("Saving graph table to path: {}", outputPath);
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//log.info("number of saved recordsa: {}", new_table.count());
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new_table
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.toJSON()
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||||
.write()
|
||||
.option("compression", "gzip")
|
||||
.text(outputPath);
|
||||
// .toJavaRDD()
|
||||
// .map(r -> OBJECT_MAPPER.writeValueAsString(r))
|
||||
// .saveAsTextFile(outputPath , GzipCodec.class);
|
||||
log.info("Saving graph table to path: {}", outputPath);
|
||||
// log.info("number of saved recordsa: {}", new_table.count());
|
||||
new_table.toJSON().write().option("compression", "gzip").text(outputPath);
|
||||
// .toJavaRDD()
|
||||
// .map(r -> OBJECT_MAPPER.writeValueAsString(r))
|
||||
// .saveAsTextFile(outputPath , GzipCodec.class);
|
||||
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
|
||||
private static <R extends Result> Dataset<Row> getPotentialResultToUpdate(SparkSession spark, String inputPath,
|
||||
Class<R> resultClazz,
|
||||
Broadcast<Dataset<DatasourceCountry>> broadcast_datasourcecountryassoc) {
|
||||
private static <R extends Result> Dataset<Row> getPotentialResultToUpdate(
|
||||
SparkSession spark,
|
||||
String inputPath,
|
||||
Class<R> resultClazz,
|
||||
Broadcast<Dataset<DatasourceCountry>> broadcast_datasourcecountryassoc) {
|
||||
|
||||
Dataset<R> result = readPathEntity(spark, inputPath, resultClazz);
|
||||
result.createOrReplaceTempView("result");
|
||||
//log.info("number of results: {}", result.count());
|
||||
// log.info("number of results: {}", result.count());
|
||||
createCfHbforresult(spark);
|
||||
return countryPropagationAssoc(spark, broadcast_datasourcecountryassoc);
|
||||
}
|
||||
|
||||
// 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 " +
|
||||
// " WHERE datainfo.deletedbyinference = false) ds " +
|
||||
// "LATERAL VIEW EXPLODE(instance) i AS inst";
|
||||
// Dataset<Row> cfhb = spark.sql(query);
|
||||
// cfhb.createOrReplaceTempView("cfhb");
|
||||
// //log.info("cfhb_number : {}", cfhb.count());
|
||||
// }
|
||||
|
||||
// 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 " +
|
||||
// " WHERE datainfo.deletedbyinference = false) ds " +
|
||||
// "LATERAL VIEW EXPLODE(instance) i AS inst";
|
||||
// Dataset<Row> cfhb = spark.sql(query);
|
||||
// cfhb.createOrReplaceTempView("cfhb");
|
||||
// //log.info("cfhb_number : {}", cfhb.count());
|
||||
// }
|
||||
|
||||
|
||||
private static Dataset<Row> countryPropagationAssoc(SparkSession spark,
|
||||
Broadcast<Dataset<DatasourceCountry>> broadcast_datasourcecountryassoc){
|
||||
private static Dataset<Row> countryPropagationAssoc(
|
||||
SparkSession spark,
|
||||
Broadcast<Dataset<DatasourceCountry>> broadcast_datasourcecountryassoc) {
|
||||
|
||||
Dataset<DatasourceCountry> datasource_country = broadcast_datasourcecountryassoc.value();
|
||||
datasource_country.createOrReplaceTempView("datasource_country");
|
||||
log.info("datasource_country number : {}",datasource_country.count());
|
||||
log.info("datasource_country number : {}", datasource_country.count());
|
||||
|
||||
String query = "SELECT id resultId, collect_set(country) countrySet "+
|
||||
"FROM ( SELECT id, country " +
|
||||
"FROM datasource_country " +
|
||||
"JOIN cfhb " +
|
||||
" ON cf = dataSourceId " +
|
||||
"UNION ALL " +
|
||||
"SELECT id , country " +
|
||||
"FROM datasource_country " +
|
||||
"JOIN cfhb " +
|
||||
" ON hb = dataSourceId ) tmp " +
|
||||
"GROUP BY id";
|
||||
String query =
|
||||
"SELECT id resultId, collect_set(country) countrySet "
|
||||
+ "FROM ( SELECT id, country "
|
||||
+ "FROM datasource_country "
|
||||
+ "JOIN cfhb "
|
||||
+ " ON cf = dataSourceId "
|
||||
+ "UNION ALL "
|
||||
+ "SELECT id , country "
|
||||
+ "FROM datasource_country "
|
||||
+ "JOIN cfhb "
|
||||
+ " ON hb = dataSourceId ) tmp "
|
||||
+ "GROUP BY id";
|
||||
Dataset<Row> potentialUpdates = spark.sql(query);
|
||||
//log.info("potential update number : {}", potentialUpdates.count());
|
||||
// log.info("potential update number : {}", potentialUpdates.count());
|
||||
return potentialUpdates;
|
||||
}
|
||||
|
||||
|
||||
|
||||
private static Dataset<DatasourceCountry> readAssocDatasourceCountry(SparkSession spark, String relationPath) {
|
||||
return spark
|
||||
.read()
|
||||
.textFile(relationPath)
|
||||
.map(value -> OBJECT_MAPPER.readValue(value, DatasourceCountry.class), Encoders.bean(DatasourceCountry.class));
|
||||
private static Dataset<DatasourceCountry> readAssocDatasourceCountry(
|
||||
SparkSession spark, String relationPath) {
|
||||
return spark.read()
|
||||
.textFile(relationPath)
|
||||
.map(
|
||||
value -> OBJECT_MAPPER.readValue(value, DatasourceCountry.class),
|
||||
Encoders.bean(DatasourceCountry.class));
|
||||
}
|
||||
|
||||
private static void writeUpdates(Dataset<ResultCountrySet> potentialUpdates, String outputPath){
|
||||
private static void writeUpdates(
|
||||
Dataset<ResultCountrySet> potentialUpdates, String outputPath) {
|
||||
potentialUpdates
|
||||
.toJSON()
|
||||
.write()
|
||||
.mode(SaveMode.Overwrite)
|
||||
.option("compression", "gzip")
|
||||
.text(outputPath);
|
||||
// map(u -> OBJECT_MAPPER.writeValueAsString(u))
|
||||
// .saveAsTextFile(outputPath, GzipCodec.class);
|
||||
// map(u -> OBJECT_MAPPER.writeValueAsString(u))
|
||||
// .saveAsTextFile(outputPath, GzipCodec.class);
|
||||
}
|
||||
|
||||
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue