forked from D-Net/dnet-hadoop
192 lines
6.4 KiB
Java
192 lines
6.4 KiB
Java
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package eu.dnetlib.doiboost.orcid;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.io.IOException;
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import java.util.*;
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import java.util.stream.Collectors;
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import java.util.stream.Stream;
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import org.apache.commons.io.IOUtils;
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import org.apache.hadoop.io.Text;
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import org.apache.hadoop.io.compress.GzipCodec;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.JavaPairRDD;
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import org.apache.spark.api.java.JavaRDD;
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import org.apache.spark.api.java.JavaSparkContext;
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import org.apache.spark.api.java.function.Function;
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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.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.esotericsoftware.minlog.Log;
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import com.google.gson.JsonElement;
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import com.google.gson.JsonParser;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.schema.orcid.AuthorData;
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import eu.dnetlib.dhp.schema.orcid.OrcidDOI;
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import eu.dnetlib.doiboost.orcid.model.WorkData;
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import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;
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import eu.dnetlib.doiboost.orcidnodoi.json.JsonWriter;
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import scala.Tuple2;
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public class SparkGenerateDoiAuthorList {
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public static void main(String[] args) throws Exception {
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Logger logger = LoggerFactory.getLogger(SparkGenerateDoiAuthorList.class);
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logger.info("[ SparkGenerateDoiAuthorList STARTED]");
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkGenerateDoiAuthorList.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/gen_doi_author_list_orcid_parameters.json")));
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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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logger.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String workingPath = parser.get("workingPath");
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logger.info("workingPath: ", workingPath);
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final String outputDoiAuthorListPath = parser.get("outputDoiAuthorListPath");
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logger.info("outputDoiAuthorListPath: ", outputDoiAuthorListPath);
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final String authorsPath = parser.get("authorsPath");
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logger.info("authorsPath: ", authorsPath);
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final String xmlWorksPath = parser.get("xmlWorksPath");
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logger.info("xmlWorksPath: ", xmlWorksPath);
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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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JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext());
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JavaPairRDD<Text, Text> summariesRDD = sc
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.sequenceFile(workingPath.concat(authorsPath), Text.class, Text.class);
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Dataset<AuthorData> summariesDataset = spark
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.createDataset(
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summariesRDD.map(seq -> loadAuthorFromJson(seq._1(), seq._2())).rdd(),
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Encoders.bean(AuthorData.class));
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JavaPairRDD<Text, Text> xmlWorksRDD = sc
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.sequenceFile(workingPath.concat(xmlWorksPath), Text.class, Text.class);
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Dataset<WorkData> activitiesDataset = spark
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.createDataset(
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xmlWorksRDD
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.map(seq -> XMLRecordParser.VTDParseWorkData(seq._2().toString().getBytes()))
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.filter(work -> work != null && work.getErrorCode() == null && work.isDoiFound())
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.rdd(),
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Encoders.bean(WorkData.class));
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Function<Tuple2<String, AuthorData>, Tuple2<String, List<AuthorData>>> toAuthorListFunction = data -> {
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try {
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String doi = data._1();
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if (doi == null) {
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return null;
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}
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AuthorData author = data._2();
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if (author == null) {
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return null;
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}
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List<AuthorData> toAuthorList = Arrays.asList(author);
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return new Tuple2<>(doi, toAuthorList);
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} catch (Exception e) {
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Log.error("toAuthorListFunction ERROR", e);
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return null;
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}
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};
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JavaRDD<Tuple2<String, List<AuthorData>>> doisRDD = activitiesDataset
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.joinWith(
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summariesDataset,
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activitiesDataset.col("oid").equalTo(summariesDataset.col("oid")), "inner")
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.map(
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(MapFunction<Tuple2<WorkData, AuthorData>, Tuple2<String, AuthorData>>) value -> {
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WorkData w = value._1;
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AuthorData a = value._2;
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return new Tuple2<>(w.getDoi(), a);
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},
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Encoders.tuple(Encoders.STRING(), Encoders.bean(AuthorData.class)))
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.filter(Objects::nonNull)
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.toJavaRDD()
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.map(toAuthorListFunction);
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JavaPairRDD
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.fromJavaRDD(doisRDD)
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.reduceByKey((d1, d2) -> {
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try {
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if (d1 != null && d2 != null) {
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Stream<AuthorData> mergedStream = Stream
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.concat(
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d1.stream(),
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d2.stream());
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List<AuthorData> mergedAuthors = mergedStream.collect(Collectors.toList());
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return mergedAuthors;
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}
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if (d1 != null) {
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return d1;
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}
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if (d2 != null) {
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return d2;
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}
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} catch (Exception e) {
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Log.error("mergeAuthorsFunction ERROR", e);
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return null;
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}
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return null;
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})
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.mapToPair(s -> {
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List<AuthorData> authorList = s._2();
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Set<String> oidsAlreadySeen = new HashSet<>();
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authorList.removeIf(a -> !oidsAlreadySeen.add(a.getOid()));
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return new Tuple2<>(s._1(), authorList);
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})
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.map(s -> {
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OrcidDOI orcidDOI = new OrcidDOI();
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orcidDOI.setDoi(s._1());
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orcidDOI.setAuthors(s._2());
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return JsonWriter.create(orcidDOI);
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})
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.saveAsTextFile(workingPath + outputDoiAuthorListPath, GzipCodec.class);
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});
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}
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private static AuthorData loadAuthorFromJson(Text orcidId, Text json) {
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AuthorData authorData = new AuthorData();
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authorData.setOid(orcidId.toString());
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JsonElement jElement = new JsonParser().parse(json.toString());
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authorData.setName(getJsonValue(jElement, "name"));
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authorData.setSurname(getJsonValue(jElement, "surname"));
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authorData.setCreditName(getJsonValue(jElement, "creditname"));
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return authorData;
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}
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private static WorkData loadWorkFromJson(Text orcidId, Text json) {
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WorkData workData = new WorkData();
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workData.setOid(orcidId.toString());
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JsonElement jElement = new JsonParser().parse(json.toString());
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workData.setDoi(getJsonValue(jElement, "doi"));
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return workData;
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}
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private static String getJsonValue(JsonElement jElement, String property) {
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if (jElement.getAsJsonObject().has(property)) {
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JsonElement name = null;
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name = jElement.getAsJsonObject().get(property);
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if (name != null && !name.isJsonNull()) {
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return name.getAsString();
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}
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}
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return null;
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}
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}
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