109 lines
3.5 KiB
Java
109 lines
3.5 KiB
Java
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package eu.dnetlib.dhp.oa.graph.clean.country;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.Serializable;
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import java.util.List;
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import java.util.Optional;
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import org.apache.commons.io.IOUtils;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.FilterFunction;
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import org.apache.spark.api.java.function.MapFunction;
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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.oa.graph.clean.CleanContextSparkJob;
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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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import scala.Tuple2;
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/**
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* @author miriam.baglioni
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* @Date 22/07/22
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*/
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public class GetDatasourceFromCountry implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(GetDatasourceFromCountry.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
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.toString(
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GetDatasourceFromCountry.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/input_datasource_country_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 = 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("inputPath");
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log.info("inputPath: {}", inputPath);
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String workingPath = parser.get("workingPath");
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log.info("workingPath: {}", workingPath);
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String country = parser.get("country");
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log.info("country: {}", country);
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SparkConf conf = new SparkConf();
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runWithSparkSession(
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conf,
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isSparkSessionManaged,
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spark -> {
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getDatasourceFromCountry(spark, country, inputPath, workingPath);
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});
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}
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private static void getDatasourceFromCountry(SparkSession spark, String country, String inputPath,
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String workingPath) {
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Dataset<Organization> organization = spark
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.read()
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.textFile(inputPath + "/organization")
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.map(
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(MapFunction<String, Organization>) value -> OBJECT_MAPPER.readValue(value, Organization.class),
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Encoders.bean(Organization.class))
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.filter(
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(FilterFunction<Organization>) o -> !o.getDataInfo().getDeletedbyinference() &&
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o.getCountry().getClassid().length() > 0 &&
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o.getCountry().getClassid().equals(country));
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;
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// filtering of the relations taking the non deleted by inference and those with IsProvidedBy as relclass
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Dataset<Relation> relation = spark
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.read()
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.textFile(inputPath + "/relation")
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.map(
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(MapFunction<String, Relation>) value -> OBJECT_MAPPER.readValue(value, Relation.class),
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Encoders.bean(Relation.class))
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.filter(
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(FilterFunction<Relation>) rel -> rel.getRelClass().equalsIgnoreCase(ModelConstants.IS_PROVIDED_BY) &&
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!rel.getDataInfo().getDeletedbyinference());
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organization
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.joinWith(relation, organization.col("id").equalTo(relation.col("target")), "left")
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.map((MapFunction<Tuple2<Organization, Relation>, String>) t2 -> t2._2().getSource(), Encoders.STRING())
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(workingPath);
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}
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}
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