96 lines
2.8 KiB
Java
96 lines
2.8 KiB
Java
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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import java.util.HashSet;
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import java.util.Set;
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import org.apache.commons.io.IOUtils;
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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.sql.*;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import scala.Tuple2;
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public class PrepareResultOrcidAssociationStep2 {
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private static final Logger log = LoggerFactory.getLogger(PrepareResultOrcidAssociationStep2.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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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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PrepareResultOrcidAssociationStep2.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/wf/subworkflows/orcidtoresultfromsemrel/input_prepareorcidtoresult_parameters2.json"));
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration);
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parser.parseArgument(args);
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Boolean isSparkSessionManaged = isSparkSessionManaged(parser);
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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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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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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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removeOutputDir(spark, outputPath);
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mergeInfo(spark, inputPath, outputPath);
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});
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}
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private static void mergeInfo(SparkSession spark, String inputPath, String outputPath) {
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Dataset<ResultOrcidList> resultOrcidAssoc = readPath(spark, inputPath + "/publication", ResultOrcidList.class)
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.union(readPath(spark, inputPath + "/dataset", ResultOrcidList.class))
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.union(readPath(spark, inputPath + "/otherresearchproduct", ResultOrcidList.class))
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.union(readPath(spark, inputPath + "/software", ResultOrcidList.class));
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resultOrcidAssoc
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.toJavaRDD()
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.mapToPair(r -> new Tuple2<>(r.getResultId(), r))
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.reduceByKey(
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(a, b) -> {
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if (a == null) {
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return b;
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}
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if (b == null) {
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return a;
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}
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Set<String> orcid_set = new HashSet<>();
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a.getAuthorList().stream().forEach(aa -> orcid_set.add(aa.getOrcid()));
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b
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.getAuthorList()
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.stream()
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.forEach(
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aa -> {
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if (!orcid_set.contains(aa.getOrcid())) {
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a.getAuthorList().add(aa);
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orcid_set.add(aa.getOrcid());
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}
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});
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return a;
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})
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.map(Tuple2::_2)
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.map(r -> OBJECT_MAPPER.writeValueAsString(r))
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.saveAsTextFile(outputPath, GzipCodec.class);
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}
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}
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