243 lines
9.0 KiB
Java
243 lines
9.0 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 static org.apache.spark.sql.functions.*;
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import java.io.IOException;
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import java.util.List;
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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.commons.lang3.StringUtils;
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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.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.sql.Dataset;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.util.LongAccumulator;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.annotation.JsonInclude;
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import com.fasterxml.jackson.databind.ObjectMapper;
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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.AuthorSummary;
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import eu.dnetlib.doiboost.orcid.xml.XMLRecordParser;
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import scala.Tuple2;
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public class SparkUpdateOrcidAuthors {
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper()
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.setSerializationInclusion(JsonInclude.Include.NON_NULL);
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public static void main(String[] args) throws IOException, Exception {
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Logger logger = LoggerFactory.getLogger(SparkUpdateOrcidAuthors.class);
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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SparkUpdateOrcidAuthors.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/doiboost/download_orcid_data.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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final String workingPath = parser.get("workingPath");
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// final String outputPath = parser.get("outputPath");
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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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LongAccumulator oldAuthorsFoundAcc = spark
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.sparkContext()
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.longAccumulator("old_authors_found");
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LongAccumulator updatedAuthorsFoundAcc = spark
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.sparkContext()
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.longAccumulator("updated_authors_found");
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LongAccumulator newAuthorsFoundAcc = spark
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.sparkContext()
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.longAccumulator("new_authors_found");
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LongAccumulator errorCodeAuthorsFoundAcc = spark
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.sparkContext()
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.longAccumulator("error_code_authors_found");
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LongAccumulator errorLoadingAuthorsJsonFoundAcc = spark
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.sparkContext()
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.longAccumulator("error_loading_authors_json_found");
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LongAccumulator errorParsingAuthorsXMLFoundAcc = spark
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.sparkContext()
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.longAccumulator("error_parsing_authors_xml_found");
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Function<Tuple2<Text, Text>, AuthorSummary> retrieveAuthorSummaryFunction = data -> {
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AuthorSummary authorSummary = new AuthorSummary();
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String orcidId = data._1().toString();
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String jsonData = data._2().toString();
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JsonElement jElement = new JsonParser().parse(jsonData);
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String statusCode = getJsonValue(jElement, "statusCode");
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String downloadDate = getJsonValue(jElement, "lastModifiedDate");
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if (statusCode.equals("200")) {
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String compressedData = getJsonValue(jElement, "compressedData");
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if (StringUtils.isEmpty(compressedData)) {
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errorLoadingAuthorsJsonFoundAcc.add(1);
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} else {
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String xmlAuthor = ArgumentApplicationParser.decompressValue(compressedData);
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try {
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authorSummary = XMLRecordParser
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.VTDParseAuthorSummary(xmlAuthor.getBytes());
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authorSummary.setStatusCode(statusCode);
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authorSummary.setDownloadDate(Long.toString(System.currentTimeMillis()));
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authorSummary.setBase64CompressData(compressedData);
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return authorSummary;
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} catch (Exception e) {
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logger.error("parsing xml " + orcidId + " [" + jsonData + "]", e);
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errorParsingAuthorsXMLFoundAcc.add(1);
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}
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}
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} else {
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authorSummary.setStatusCode(statusCode);
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authorSummary.setDownloadDate(Long.toString(System.currentTimeMillis()));
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errorCodeAuthorsFoundAcc.add(1);
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}
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return authorSummary;
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};
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Dataset<AuthorSummary> downloadedAuthorSummaryDS = spark
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.createDataset(
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sc
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.sequenceFile(workingPath + "downloads/updated_authors/*", Text.class, Text.class)
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.map(retrieveAuthorSummaryFunction)
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.rdd(),
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Encoders.bean(AuthorSummary.class));
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Dataset<AuthorSummary> currentAuthorSummaryDS = spark
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.createDataset(
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sc
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.textFile(workingPath.concat("orcid_dataset/authors/*"))
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.map(item -> OBJECT_MAPPER.readValue(item, AuthorSummary.class))
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.rdd(),
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Encoders.bean(AuthorSummary.class));
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Dataset<AuthorSummary> mergedAuthorSummaryDS = currentAuthorSummaryDS
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.joinWith(
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downloadedAuthorSummaryDS,
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currentAuthorSummaryDS
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.col("authorData.oid")
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.equalTo(downloadedAuthorSummaryDS.col("authorData.oid")),
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"full_outer")
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.map(value -> {
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Optional<AuthorSummary> opCurrent = Optional.ofNullable(value._1());
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Optional<AuthorSummary> opDownloaded = Optional.ofNullable(value._2());
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if (!opCurrent.isPresent()) {
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newAuthorsFoundAcc.add(1);
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return opDownloaded.get();
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}
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if (!opDownloaded.isPresent()) {
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oldAuthorsFoundAcc.add(1);
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return opCurrent.get();
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}
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if (opCurrent.isPresent() && opDownloaded.isPresent()) {
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updatedAuthorsFoundAcc.add(1);
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return opDownloaded.get();
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}
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return null;
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},
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Encoders.bean(AuthorSummary.class))
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.filter(Objects::nonNull);
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long mergedCount = mergedAuthorSummaryDS.count();
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Dataset<AuthorSummary> base64DedupedDS = mergedAuthorSummaryDS.dropDuplicates("base64CompressData");
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List<String> dupOids = base64DedupedDS
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.groupBy("authorData.oid")
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.agg(count("authorData.oid").alias("oidOccurrenceCount"))
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.where("oidOccurrenceCount > 1")
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.select("oid")
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.toJavaRDD()
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.map(row -> row.get(0).toString())
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.collect();
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JavaRDD<AuthorSummary> dupAuthors = base64DedupedDS
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.toJavaRDD()
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.filter(
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authorSummary -> (Objects.nonNull(authorSummary.getAuthorData())
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&& Objects.nonNull(authorSummary.getAuthorData().getOid())))
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.filter(authorSummary -> dupOids.contains(authorSummary.getAuthorData().getOid()));
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Dataset<AuthorSummary> dupAuthorSummaryDS = spark
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.createDataset(
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dupAuthors.rdd(),
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Encoders.bean(AuthorSummary.class));
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List<Tuple2<String, String>> lastModifiedAuthors = dupAuthorSummaryDS
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.groupBy("authorData.oid")
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.agg(array_max(collect_list("downloadDate")))
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.map(
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row -> new Tuple2<>(row.get(0).toString(), row.get(1).toString()),
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Encoders.tuple(Encoders.STRING(), Encoders.STRING()))
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.toJavaRDD()
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.collect();
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JavaRDD<AuthorSummary> lastDownloadedAuthors = base64DedupedDS
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.toJavaRDD()
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.filter(
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authorSummary -> (Objects.nonNull(authorSummary.getAuthorData())
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&& Objects.nonNull(authorSummary.getAuthorData().getOid())))
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.filter(authorSummary -> {
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boolean oidFound = lastModifiedAuthors
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.stream()
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.filter(a -> a._1().equals(authorSummary.getAuthorData().getOid()))
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.count() == 1;
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boolean tsFound = lastModifiedAuthors
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.stream()
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.filter(
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a -> a._1().equals(authorSummary.getAuthorData().getOid()) &&
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a._2().equals(authorSummary.getDownloadDate()))
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.count() == 1;
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return (oidFound && tsFound) || (!oidFound);
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});
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Dataset<AuthorSummary> cleanedDS = spark
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.createDataset(
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lastDownloadedAuthors.rdd(),
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Encoders.bean(AuthorSummary.class))
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.dropDuplicates("downloadDate", "authorData");
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cleanedDS
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.toJavaRDD()
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.map(authorSummary -> OBJECT_MAPPER.writeValueAsString(authorSummary))
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.saveAsTextFile(workingPath.concat("orcid_dataset/new_authors"), GzipCodec.class);
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long cleanedDSCount = cleanedDS.count();
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logger.info("report_oldAuthorsFoundAcc: " + oldAuthorsFoundAcc.value().toString());
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logger.info("report_newAuthorsFoundAcc: " + newAuthorsFoundAcc.value().toString());
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logger.info("report_updatedAuthorsFoundAcc: " + updatedAuthorsFoundAcc.value().toString());
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logger.info("report_errorCodeFoundAcc: " + errorCodeAuthorsFoundAcc.value().toString());
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logger.info("report_errorLoadingJsonFoundAcc: " + errorLoadingAuthorsJsonFoundAcc.value().toString());
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logger.info("report_errorParsingXMLFoundAcc: " + errorParsingAuthorsXMLFoundAcc.value().toString());
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logger.info("report_merged_count: " + mergedCount);
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logger.info("report_cleaned_count: " + cleanedDSCount);
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});
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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 "";
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}
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}
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