134 lines
5.6 KiB
Java
134 lines
5.6 KiB
Java
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package eu.dnetlib.dhp.oa.graph.dump.filterentities;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.*;
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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.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 static org.apache.spark.sql.functions.expr;
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import static org.apache.spark.sql.functions.max;
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import static org.apache.spark.sql.functions.col;
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import java.io.Serializable;
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import java.util.Optional;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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/**
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* @author miriam.baglioni
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* @Date 20/03/24
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*/
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public class SelectLOT1Entities implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SelectLOT1Entities.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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FilterEntities.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump/skgif/eosc_entities_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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final String inputPath = parser.get("sourcePath");
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log.info("inputPath: {}", inputPath);
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final String filterPath = parser.get("filterPath");
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log.info("filterPath: {}", filterPath);
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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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selectEntities(spark, inputPath, filterPath);
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});
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}
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private static <R extends Result> void selectEntities(SparkSession spark, String inputPath, String filterPath) {
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selectPublications(spark,inputPath,filterPath);
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selectDataset(spark,inputPath,filterPath);
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selectSoftware(spark,inputPath,filterPath);
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selectOthers(spark,inputPath,filterPath);
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}
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private static void selectOthers(SparkSession spark, String inputPath, String filterPath) {
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spark.read().schema(Encoders.bean(OtherResearchProduct.class).schema())
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.json(inputPath + "otherresearchproduct")
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.where("datainfo.deletedbyinference != true AND datainfo.invisible != true")
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.selectExpr("id", "instance", "explode(pid) as pid").where("pid.qualifier.classid IN ('doi', 'handle')") // filter by pid type
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.selectExpr("id", "explode(instance) as instance")
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.withColumn("CCL", expr("CASE WHEN instance.license.value LIKE 'CC%' OR instance.license.value LIKE '%/creativecommons.org/%' THEN 1 ELSE 0 END"))
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.groupBy("id")
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.agg(max(col("CCL")).as("CCL"))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.parquet(filterPath + "otherresearchproduct_ids");
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}
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private static void selectSoftware(SparkSession spark, String inputPath, String filterPath) {
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spark.read().schema(Encoders.bean(Software.class).schema())
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.json(inputPath + "software")
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.where("datainfo.deletedbyinference != true AND datainfo.invisible != true")
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.selectExpr("id", "instance", "explode(pid) as pid").where("pid.qualifier.classid IN ('doi', 'swhid')") // filter by pid type
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.selectExpr("id", "explode(instance) as instance")
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.withColumn("CCL", expr("CASE WHEN instance.license.value LIKE 'CC%' OR instance.license.value LIKE '%/creativecommons.org/%' THEN 1 ELSE 0 END"))
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.groupBy("id")
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.agg(max(col("CCL")).as("CCL"))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.parquet(filterPath + "software_ids");
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}
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private static void selectDataset(SparkSession spark, String inputPath, String filterPath) {
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spark.read().schema(Encoders.bean(Dataset.class).schema())
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.json(inputPath + "dataset")
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.where("datainfo.deletedbyinference != true AND datainfo.invisible != true")
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.selectExpr("id", "instance", "explode(pid) as pid").where("pid.qualifier.classid IN ('doi', 'handle', 'pdb', 'ena', 'uniprot')") // filter by pid type
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.selectExpr("id", "explode(instance) as instance")
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.withColumn("CCL", expr("CASE WHEN instance.license.value LIKE 'CC%' OR instance.license.value LIKE '%/creativecommons.org/%' THEN 1 ELSE 0 END"))
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.groupBy("id")
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.agg(max(col("CCL")).as("CCL"))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.parquet(filterPath + "dataset_ids");
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}
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private static void selectPublications(SparkSession spark, String inputPath, String filterPath) {
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spark.read().schema(Encoders.bean(Publication.class).schema())
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.json(inputPath + "publication")
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.where("datainfo.deletedbyinference != true AND datainfo.invisible != true")
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.selectExpr("id", "instance", "explode(pid) as pid").where("pid.qualifier.classid IN ('doi', 'arXiv', 'pmid', 'handle')") // filter by pid type
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.selectExpr("id", "explode(instance) as instance").where("instance.instancetype.classname IN('Book', 'Article', 'Journal', 'Data Paper', 'Software Paper', 'Preprint', 'Part of book or chapter of book', 'Thesis', 'Master thesis', 'Bachelor thesis', 'Doctoral thesis', 'Conference object', 'Research', 'Other literature type')")
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.withColumn("CCL", expr("CASE WHEN instance.license.value LIKE 'CC%' OR instance.license.value LIKE '%/creativecommons.org/%' THEN 1 ELSE 0 END"))
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.groupBy("id")
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.agg(max(col("CCL")).as("CCL"))
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.write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.parquet(filterPath + "publication_ids");
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}
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}
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