123 lines
4.4 KiB
Java
123 lines
4.4 KiB
Java
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package eu.dnetlib.doiboost.orcidnodoi;
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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.Objects;
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import java.util.Optional;
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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.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.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.google.gson.Gson;
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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.doiboost.orcid.model.AuthorData;
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import eu.dnetlib.doiboost.orcidnodoi.model.WorkDataNoDoi;
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import eu.dnetlib.doiboost.orcidnodoi.similarity.AuthorMatcher;
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import scala.Tuple2;
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public class SparkGenEnrichedOrcidWorks {
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public static void main(String[] args) throws IOException, Exception {
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Logger logger = LoggerFactory.getLogger(SparkGenEnrichedOrcidWorks.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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SparkGenEnrichedOrcidWorks.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/gen_enriched_orcid_works_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 outputEnrichedWorksPath = parser.get("outputEnrichedWorksPath");
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logger.info("outputEnrichedWorksPath: ", outputEnrichedWorksPath);
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final String outputWorksPath = parser.get("outputWorksPath");
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logger.info("outputWorksPath: ", outputWorksPath);
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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 + "../orcid_summaries/output/authors.seq", 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> activitiesRDD = sc
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.sequenceFile(workingPath + outputWorksPath + "works_X.seq", Text.class, Text.class);
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Dataset<WorkDataNoDoi> activitiesDataset = spark
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.createDataset(
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activitiesRDD.map(seq -> loadWorkFromJson(seq._1(), seq._2())).rdd(),
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Encoders.bean(WorkDataNoDoi.class));
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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<WorkDataNoDoi, AuthorData>, Tuple2<String, WorkDataNoDoi>>) value -> {
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WorkDataNoDoi w = value._1;
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AuthorData a = value._2;
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AuthorMatcher.match(a, w.getContributors());
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return new Tuple2<>(a.getOid(), w);
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},
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Encoders.tuple(Encoders.STRING(), Encoders.bean(WorkDataNoDoi.class)))
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.filter(Objects::nonNull)
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.toJavaRDD()
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.saveAsTextFile(workingPath + outputEnrichedWorksPath);
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;
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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 WorkDataNoDoi loadWorkFromJson(Text orcidId, Text json) {
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WorkDataNoDoi workData = new Gson().fromJson(json.toString(), WorkDataNoDoi.class);
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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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