forked from D-Net/dnet-hadoop
122 lines
4.0 KiB
Java
122 lines
4.0 KiB
Java
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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 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.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.SaveMode;
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import org.apache.spark.sql.SparkSession;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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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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/**
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* For the association of the country to the datasource The association is computed only for datasource of specific type
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* or having whitelisted ids The country is registered in the Organization associated to the Datasource, so the relation
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* provides between Datasource and 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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public static void main(String[] args) throws Exception {
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String jsonConfiguration = IOUtils
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.toString(
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PrepareDatasourceCountryAssociation.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/countrypropagation/input_prepareassoc_parameters.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
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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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final String outputPath = parser.get("outputPath");
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log.info("outputPath {}: ", outputPath);
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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(
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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(
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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(
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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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whitelisted += " OR id = '" + i + "'";
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}
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Dataset<Datasource> datasource = readPath(spark, inputPath + "/datasource", Datasource.class);
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Dataset<Relation> relation = readPath(spark, inputPath + "/relation", Relation.class);
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Dataset<Organization> organization = readPath(spark, inputPath + "/organization", 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 "
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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
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.sql(query)
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.as(Encoders.bean(DatasourceCountry.class))
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.write()
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.option("compression", "gzip")
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.mode(SaveMode.Overwrite)
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.json(outputPath);
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}
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}
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