143 lines
4.9 KiB
Java
143 lines
4.9 KiB
Java
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package eu.dnetlib.dhp.oa.graph.dump.pid;
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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.ArrayList;
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import java.util.List;
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import java.util.Optional;
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import java.util.stream.Collectors;
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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.FlatMapFunction;
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import org.apache.spark.api.java.function.MapFunction;
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import org.apache.spark.sql.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.google.gson.Gson;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.oa.graph.dump.Utils;
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import eu.dnetlib.dhp.schema.dump.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.dump.pidgraph.Entity;
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import eu.dnetlib.dhp.schema.oaf.OtherResearchProduct;
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import eu.dnetlib.dhp.schema.oaf.Publication;
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import eu.dnetlib.dhp.schema.oaf.Software;
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public class SparkDumpPidAuthor implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(SparkDumpPidAuthor.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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SparkDumpPidAuthor.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/oa/graph/dump_pid/input_dump_author.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 outputPath = parser.get("outputPath");
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log.info("outputPath: {}", outputPath);
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final List<String> allowedAuthorPids = new Gson().fromJson(parser.get("allowedAuthorPids"), List.class);
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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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Utils.removeOutputDir(spark, outputPath);
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dumpPidAuthor(spark, inputPath, outputPath, allowedAuthorPids);
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});
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}
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private static void dumpPidAuthor(SparkSession spark, String inputPath, String outputPath, List<String> aap) {
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Dataset<Publication> publication = Utils.readPath(spark, inputPath + "/publication", Publication.class);
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Dataset<eu.dnetlib.dhp.schema.oaf.Dataset> dataset = Utils
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.readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class);
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Dataset<Software> software = Utils.readPath(spark, inputPath + "/software", Software.class);
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Dataset<OtherResearchProduct> other = Utils
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.readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class);
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publication.createOrReplaceTempView("publication");
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dataset.createOrReplaceTempView("dataset");
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software.createOrReplaceTempView("software");
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other.createOrReplaceTempView("other");
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Dataset<KeyValue> pids = spark
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.sql(
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"SELECT DISTINCT apid.value value , apid.qualifier.classid key " +
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"FROM publication " +
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"LATERAL VIEW EXPLODE (author) a as auth " +
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"LATERAL VIEW EXPLODE (auth.pid) p as apid ")
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.as(Encoders.bean(KeyValue.class))
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.union(
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spark
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.sql(
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"SELECT DISTINCT apid.value value , apid.qualifier.classid key " +
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"FROM dataset " +
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"LATERAL VIEW EXPLODE (author) a as auth " +
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"LATERAL VIEW EXPLODE (auth.pid) p as apid ")
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.as(Encoders.bean(KeyValue.class)))
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.union(
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spark
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.sql(
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"SELECT DISTINCT apid.value value , apid.qualifier.classid key " +
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"FROM software " +
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"LATERAL VIEW EXPLODE (author) a as auth " +
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"LATERAL VIEW EXPLODE (auth.pid) p as apid ")
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.as(Encoders.bean(KeyValue.class)))
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.union(
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spark
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.sql(
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"SELECT DISTINCT apid.value value , apid.qualifier.classid key " +
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"FROM other " +
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"LATERAL VIEW EXPLODE (author) a as auth " +
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"LATERAL VIEW EXPLODE (auth.pid) p as apid ")
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.as(Encoders.bean(KeyValue.class)));
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pids.createOrReplaceTempView("pids");
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spark
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.sql(
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"Select distinct key, value " +
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"FROM pids")
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.as(Encoders.bean(KeyValue.class))
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.filter((FilterFunction<KeyValue>) p -> aap.contains(p.getKey()))
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.map(
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(MapFunction<KeyValue, Entity>) pid -> Entity.newInstance(pid.getKey() + ":" + pid.getValue()),
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Encoders.bean(Entity.class))
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.write()
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// resultPids.flatMap((FlatMapFunction<ResultPidsList, Entity>) r-> {
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// List<Entity> ret = new ArrayList<>();
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// r.getAuthorAllowedPids().forEach(pid -> {
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// ret.addAll(pid.stream().map(p -> Entity.newInstance(p.getKey() + ":" + p.getValue())).collect(Collectors.toList()));
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//
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// });
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// return ret.iterator();
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// }, Encoders.bean(Entity.class))
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// .write()
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.mode(SaveMode.Overwrite)
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.option("compression", "gzip")
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.json(outputPath + "/author");
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}
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}
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