130 lines
5.0 KiB
Java
130 lines
5.0 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.runWithSparkSession;
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import java.util.Arrays;
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import java.util.List;
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import com.fasterxml.jackson.databind.ObjectMapper;
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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.ForeachFunction;
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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 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.Datasource;
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import eu.dnetlib.dhp.schema.oaf.Organization;
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import eu.dnetlib.dhp.schema.oaf.Qualifier;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import scala.Tuple2;
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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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runWithSparkSession(
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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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// filtering of the datasource taking only the non deleted by inference and those with the allowed types or
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// whose id is in whitelist
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Dataset<Datasource> datasource = readPath(spark, inputPath + "/datasource", Datasource.class)
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.filter(
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(FilterFunction<Datasource>) ds -> !ds.getDataInfo().getDeletedbyinference() &&
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(allowedtypes.contains(ds.getDatasourcetype().getClassid()) ||
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whitelist.contains(ds.getId())));
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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 = readPath(spark, inputPath + "/relation", 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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// filtering of the organization taking only the non deleted by inference and those with information about the
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// country
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Dataset<Organization> organization = readPath(spark, inputPath + "/organization", 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(ModelConstants.UNKNOWN)) ;
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// associated the datasource id with the id of the organization providing the datasource
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Dataset<EntityEntityRel> dse = datasource
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.joinWith(relation, datasource.col("id").equalTo(relation.col("source")))
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.map(
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(MapFunction<Tuple2<Datasource, Relation>, EntityEntityRel>) t2 -> EntityEntityRel
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.newInstance(t2._2.getSource(), t2._2.getTarget()),
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Encoders.bean(EntityEntityRel.class));
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// joins with the information stored in the organization dataset to associate the country to the datasource id
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dse
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.joinWith(organization, dse.col("entity2Id").equalTo(organization.col("id")))
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.map((MapFunction<Tuple2<EntityEntityRel, Organization>, DatasourceCountry>) t2 -> {
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Qualifier country = t2._2.getCountry();
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return DatasourceCountry
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.newInstance(
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t2._1.getEntity1Id(),
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CountrySbs.newInstance(country.getClassid(), country.getClassname()));
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}, 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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