selection of the results id having the given country among the countries, or being in relation with other entities associated with the given country

This commit is contained in:
Miriam Baglioni 2023-04-27 18:14:48 +02:00
parent 1671e78e59
commit 7f57f3cd1e
1 changed files with 157 additions and 0 deletions

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package eu.dnetlib.dhp.oa.graph.dump.country;
import eu.dnetlib.dhp.application.ArgumentApplicationParser;
import eu.dnetlib.dhp.oa.graph.dump.Utils;
import eu.dnetlib.dhp.schema.common.ModelConstants;
import eu.dnetlib.dhp.schema.oaf.*;
import org.apache.commons.io.IOUtils;
import org.apache.spark.SparkConf;
import org.apache.spark.api.java.function.FilterFunction;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Dataset;
import org.apache.spark.sql.Encoders;
import org.apache.spark.sql.SaveMode;
import org.apache.spark.sql.SparkSession;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.xml.sax.SAXException;
import scala.Tuple2;
import java.io.Serializable;
import java.io.StringReader;
import java.util.*;
import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
/**
* @author miriam.baglioni
* @Date 27/04/23
* Finds the results id which are in relation with another entity having the given country
* or that have that country in the country list
*/
public class SparkFindResultsRelatedToCountry implements Serializable {
private static final Logger log = LoggerFactory.getLogger(SparkFindResultsRelatedToCountry.class);
public static final String COMPRESSION = "compression";
public static final String GZIP = "gzip";
public static void main(String[] args) throws Exception {
String jsonConfiguration = IOUtils
.toString(
SparkFindResultsRelatedToCountry.class
.getResourceAsStream(
"/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json"));
final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
parser.parseArgument(args);
Boolean isSparkSessionManaged = Optional
.ofNullable(parser.get("isSparkSessionManaged"))
.map(Boolean::valueOf)
.orElse(Boolean.TRUE);
log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
final String inputPath = parser.get("sourcePath");
log.info("inputPath: {}", inputPath);
final String outputPath = parser.get("outputPath");
log.info("outputPath: {}", outputPath);
final String country = parser.get("country");
run(
isSparkSessionManaged, inputPath, outputPath, country);
}
private static void run(Boolean isSparkSessionManaged, String inputPath, String outputPath,
String country) {
SparkConf conf = new SparkConf();
runWithSparkSession(
conf,
isSparkSessionManaged,
spark -> {
findRelatedEntities(
spark, inputPath, outputPath, country);
});
}
public static <I extends eu.dnetlib.dhp.schema.oaf.Result> void findRelatedEntities(
SparkSession spark,
String inputPath,
String outputPath,
String country) {
Dataset<Project> projectsInCountry = Utils.readPath(spark, inputPath + "/project", Project.class)
.filter((FilterFunction<Project>) p -> isCountryInFunderJurisdiction(p.getFundingtree(), country));
Dataset<Relation> relsProjectResults = Utils.readPath(spark, inputPath + "/relation", Relation.class)
.filter((FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
r.getRelClass().equals(ModelConstants.PRODUCES));
projectsInCountry.joinWith(relsProjectResults, projectsInCountry.col("id").equalTo(relsProjectResults.col("source")))
.map((MapFunction<Tuple2<Project, Relation>, String>) t2 -> t2._2().getTarget(), Encoders.STRING())
.write()
.option(COMPRESSION, GZIP)
.mode(SaveMode.Overwrite)
.json(outputPath );
Dataset<Organization> organizationsInCountry = Utils.readPath(spark, inputPath + "/organization", Organization.class)
.filter((FilterFunction<Organization>) o -> o.getCountry().getClassid().equals(country));
Dataset<Relation> relsOrganizationResults = Utils.readPath(spark, inputPath + "/relation", Relation.class)
.filter((FilterFunction<Relation>) r -> !r.getDataInfo().getDeletedbyinference() &&
r.getRelClass().equals(ModelConstants.IS_AUTHOR_INSTITUTION_OF));
organizationsInCountry.joinWith(relsOrganizationResults, organizationsInCountry.col("id").equalTo(relsOrganizationResults.col("source")))
.map((MapFunction<Tuple2<Organization, Relation>, String>) t2 -> t2._2().getTarget(), Encoders.STRING())
.write()
.option(COMPRESSION, GZIP)
.mode(SaveMode.Append)
.json(outputPath );
selectResultWithCountry(spark, inputPath, outputPath, country, "publication", Publication.class);
selectResultWithCountry(spark, inputPath, outputPath, country, "dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class);
selectResultWithCountry(spark, inputPath, outputPath, country, "software", Software.class);
selectResultWithCountry(spark, inputPath, outputPath, country, "otherresearchproduct", OtherResearchProduct.class);
}
private static <R extends Result> void selectResultWithCountry(SparkSession spark, String inputPath, String outputPath, String country, String type, Class<R> inputClazz) {
Utils.readPath(spark, inputPath + "/" + type, inputClazz)
.filter((FilterFunction<R>) p -> !p.getDataInfo().getDeletedbyinference() && !p.getDataInfo().getInvisible() &&
p.getCountry().stream().anyMatch(c -> c.getClassid().equals(country)))
.map((MapFunction<R, String>) p -> p.getId(), Encoders.STRING() )
.write()
.option(COMPRESSION, GZIP)
.mode(SaveMode.Append)
.json(outputPath);
}
private static boolean isCountryInFunderJurisdiction(List<Field<String>> fundingtrees, String country) {
try {
final SAXReader reader = new SAXReader();
reader.setFeature("http://apache.org/xml/features/disallow-doctype-decl", true);
for (Field<String> fundingtree: fundingtrees){
final Document doc = reader.read(new StringReader(fundingtree.getValue()));
if(((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText().equals(country)){
return true;
}
}
return false;
} catch (DocumentException | SAXException e) {
throw new IllegalArgumentException(e);
}
}
}