121 lines
4.1 KiB
Java
121 lines
4.1 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.common.ModelConstants;
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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 = " d.id = '" + whitelist.get(0) + "'";
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for (int i = 1; i < whitelist.size(); i++) {
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whitelisted += " OR d.id = '" + whitelist.get(i) + "'";
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}
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String allowed = "d.datasourcetype.classid = '" + allowedtypes.get(0) + "'";
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for (int i = 1; i < allowedtypes.size(); i++) {
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allowed += " OR d.datasourcetype.classid = '" + allowedtypes.get(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, " +
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"named_struct('classid', country.classid, 'classname', country.classname) country " +
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"FROM datasource d " +
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"JOIN relation rel " +
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"ON d.id = rel.source " +
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"JOIN organization o " +
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"ON o.id = rel.target " +
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"WHERE rel.datainfo.deletedbyinference = false " +
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"and lower(rel.relclass) = '" + ModelConstants.IS_PROVIDED_BY.toLowerCase() + "'" +
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"and o.datainfo.deletedbyinference = false " +
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"and length(o.country.classid) > 0 " +
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"and (" + allowed + " or " + whitelisted + ")";
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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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