forked from D-Net/dnet-hadoop
398 lines
19 KiB
Java
398 lines
19 KiB
Java
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package eu.dnetlib.dhp.orcidtoresultfromsemrel;
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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 eu.dnetlib.dhp.schema.oaf.*;
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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.fs.FileSystem;
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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.JavaSparkContext;
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import org.apache.spark.sql.Encoders;
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import org.apache.spark.sql.Row;
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import org.apache.spark.sql.SparkSession;
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import scala.Tuple2;
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import java.util.*;
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import static eu.dnetlib.dhp.PropagationConstant.*;
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public class SparkOrcidToResultFromSemRelJob2 {
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public static void main(String[] args) throws Exception {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(IOUtils.toString(SparkOrcidToResultFromSemRelJob2.class.getResourceAsStream("/eu/dnetlib/dhp/orcidtoresultfromremrel/input_orcidtoresult_parameters.json")));
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parser.parseArgument(args);
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SparkConf conf = new SparkConf();
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conf.set("hive.metastore.uris", parser.get("hive_metastore_uris"));
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final SparkSession spark = SparkSession
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.builder()
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.appName(SparkOrcidToResultFromSemRelJob2.class.getSimpleName())
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.master(parser.get("master"))
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.config(conf)
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.enableHiveSupport()
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.getOrCreate();
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final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext());
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final String inputPath = parser.get("sourcePath");
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final String outputPath = "/tmp/provision/propagation/orcidtoresult";
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final List<String> allowedsemrel = Arrays.asList(parser.get("allowedsemrels").split(";"));
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boolean writeUpdate = TRUE.equals(parser.get("writeUpdate"));
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boolean saveGraph = TRUE.equals(parser.get("saveGraph"));
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createOutputDirs(outputPath, FileSystem.get(spark.sparkContext().hadoopConfiguration()));
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org.apache.spark.sql.Dataset<Relation> relation = spark.createDataset(sc.textFile(inputPath + "/relation")
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.map(item -> new ObjectMapper().readValue(item, Relation.class)).rdd(), Encoders.bean(Relation.class));
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org.apache.spark.sql.Dataset<Dataset> dataset = spark.createDataset(sc.textFile(inputPath + "/dataset")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Dataset.class)).rdd(),
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Encoders.bean(eu.dnetlib.dhp.schema.oaf.Dataset.class));
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org.apache.spark.sql.Dataset<OtherResearchProduct> other = spark.createDataset(sc.textFile(inputPath + "/otherresearchproduct")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class)).rdd(),
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Encoders.bean(eu.dnetlib.dhp.schema.oaf.OtherResearchProduct.class));
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org.apache.spark.sql.Dataset<Software> software = spark.createDataset(sc.textFile(inputPath + "/software")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Software.class)).rdd(),
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Encoders.bean(eu.dnetlib.dhp.schema.oaf.Software.class));
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org.apache.spark.sql.Dataset<Publication> publication = spark.createDataset(sc.textFile(inputPath + "/publication")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Publication.class)).rdd(),
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Encoders.bean(eu.dnetlib.dhp.schema.oaf.Publication.class));
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relation.createOrReplaceTempView("relation");
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String query = "Select source, target " +
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"from relation " +
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"where datainfo.deletedbyinference = false " + getConstraintList(" relclass = '" , allowedsemrel);
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org.apache.spark.sql.Dataset<Row> result_result = spark.sql(query);
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publication.createOrReplaceTempView("publication");
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org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid = getResultWithOrcid("publication", spark)
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.as(Encoders.bean(ResultWithOrcid.class));
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dataset.createOrReplaceTempView("dataset");
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org.apache.spark.sql.Dataset<ResultWithOrcid> dats_with_orcid = getResultWithOrcid("dataset", spark)
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.as(Encoders.bean(ResultWithOrcid.class));
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other.createOrReplaceTempView("orp");
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org.apache.spark.sql.Dataset<ResultWithOrcid> orp_with_orcid = getResultWithOrcid("orp", spark)
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.as(Encoders.bean(ResultWithOrcid.class));
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dataset.createOrReplaceTempView("software");
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org.apache.spark.sql.Dataset<ResultWithOrcid> software_with_orcid = getResultWithOrcid("software", spark)
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.as(Encoders.bean(ResultWithOrcid.class));
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//get the results having at least one author pid we are interested in
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//target of the relation from at least one source with orcid.
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//the set of authors contains all those that have orcid and are related to target
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//from any source with allowed semantic relationship
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JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_pubs = getTargetAutoritativeAuthorList(pubs_with_orcid);
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JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_dats = getTargetAutoritativeAuthorList(dats_with_orcid);
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JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_orp = getTargetAutoritativeAuthorList(orp_with_orcid);
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JavaPairRDD<String, List<AutoritativeAuthor>> target_authorlist_from_sw = getTargetAutoritativeAuthorList(software_with_orcid);
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if(writeUpdate){
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target_authorlist_from_dats.map(r -> new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath + "/" + "update_dats");
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target_authorlist_from_pubs.map(r -> new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath + "/" + "update_pubs");
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target_authorlist_from_orp.map(r -> new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath + "/" + "update_orp");
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target_authorlist_from_sw.map(r -> new ObjectMapper().writeValueAsString(r))
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.saveAsTextFile(outputPath + "/" + "update_sw");
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}
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if(saveGraph){
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sc.textFile(inputPath + "/publication")
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.map(item -> new ObjectMapper().readValue(item, eu.dnetlib.dhp.schema.oaf.Publication.class))
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.mapToPair(p -> new Tuple2<>(p.getId(),p))
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.leftOuterJoin(target_authorlist_from_pubs)
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.map(c -> {
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Result r = c._2()._1();
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if(!c._2()._2().isPresent()){
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return r;
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}
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List<eu.dnetlib.dhp.schema.oaf.Author> toenrich_author = r.getAuthor();
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List<AutoritativeAuthor> autoritativeAuthors = c._2()._2().get();
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for(eu.dnetlib.dhp.schema.oaf.Author author: toenrich_author){
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if (!containsAllowedPid(author)){
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enrichAuthor(author, autoritativeAuthors);
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}
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}
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return r;
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});
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}
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}
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private static void enrichAuthor(eu.dnetlib.dhp.schema.oaf.Author a, List<AutoritativeAuthor> au){
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for (AutoritativeAuthor aa: au){
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if(enrichAuthor(aa, a)){
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return;
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}
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}
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}
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// private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritativeAuthorList(org.apache.spark.sql.Dataset<Row> result_result, org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid) {
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// return pubs_with_orcid
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// .toJavaRDD()
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// .mapToPair(p -> new Tuple2<>(p.getId(), p.getAuthorList()))
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// .join(result_result.toJavaRDD().mapToPair(rel -> new Tuple2<>(rel.getString(0), rel.getString(1))))
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// .mapToPair(c -> new Tuple2<>(c._2._2(), c._2()._1()))
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// .reduceByKey((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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//
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// Set<String> authSet = new HashSet<>();
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// a.stream().forEach(au -> authSet.add(au.getOrcid()));
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//
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// b.stream().forEach(au -> {
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// if (!authSet.contains(au.getOrcid())) {
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// a.add(au);
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// }
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// }
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// );
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// return a;
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// });
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// }
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private static JavaPairRDD<String, List<AutoritativeAuthor>> getTargetAutoritativeAuthorList( org.apache.spark.sql.Dataset<ResultWithOrcid> pubs_with_orcid) {
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return pubs_with_orcid
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.toJavaRDD()
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.mapToPair(p -> new Tuple2<>(p.getId(), p.getAuthorList()))
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.reduceByKey((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> authSet = new HashSet<>();
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a.stream().forEach(au -> authSet.add(au.getOrcid()));
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b.stream().forEach(au -> {
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if (!authSet.contains(au.getOrcid())) {
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a.add(au);
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}
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}
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);
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return a;
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});
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}
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private static org.apache.spark.sql.Dataset<Row> getResultWithOrcid(String table, SparkSession spark){
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String query = " select target, author " +
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" from (select id, collect_set(named_struct('name', name, 'surname', surname, 'fullname', fullname, 'orcid', orcid)) author " +
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" from ( " +
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" select id, MyT.fullname, MyT.name, MyT.surname, MyP.value orcid " +
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" from " + table +
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" lateral view explode (author) a as MyT " +
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" lateral view explode (MyT.pid) p as MyP " +
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" where MyP.qualifier.classid = 'ORCID') tmp " +
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" group by id) r_t " +
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" join (" +
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" select source, target " +
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" from relation " +
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" where datainfo.deletedbyinference = false and (relclass = 'isSupplementedBy' or relclass = 'isSupplementTo') rel_rel " +
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" on source = id";
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return spark.sql(query);
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}
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private static boolean enrichAuthor(AutoritativeAuthor autoritative_author, eu.dnetlib.dhp.schema.oaf.Author author) {
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boolean toaddpid = false;
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if (StringUtils.isNoneEmpty(autoritative_author.getSurname())) {
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if (StringUtils.isNoneEmpty(author.getSurname())) {
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if (autoritative_author.getSurname().trim().equalsIgnoreCase(author.getSurname().trim())) {
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//have the same surname. Check the name
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if (StringUtils.isNoneEmpty(autoritative_author.getName())) {
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if (StringUtils.isNoneEmpty(author.getName())) {
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if (autoritative_author.getName().trim().equalsIgnoreCase(author.getName().trim())) {
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toaddpid = true;
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}
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//they could be differently written (i.e. only the initials of the name in one of the two
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if (autoritative_author.getName().trim().substring(0, 0).equalsIgnoreCase(author.getName().trim().substring(0, 0))) {
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toaddpid = true;
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}
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}
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}
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}
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}
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}
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if (toaddpid){
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StructuredProperty pid = new StructuredProperty();
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String aa_pid = autoritative_author.getOrcid();
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pid.setValue(aa_pid);
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pid.setQualifier(getQualifier(PROPAGATION_AUTHOR_PID, PROPAGATION_AUTHOR_PID ));
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pid.setDataInfo(getDataInfo(PROPAGATION_DATA_INFO_TYPE, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_ID, PROPAGATION_ORCID_TO_RESULT_FROM_SEM_REL_CLASS_NAME));
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if(author.getPid() == null){
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author.setPid(Arrays.asList(pid));
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}else{
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author.getPid().add(pid);
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}
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}
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return toaddpid;
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}
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// private static List<Author> enrichAuthors(List<Author> autoritative_authors, List<Author> to_enrich_authors, boolean filter){
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//// List<Author> autoritative_authors = p._2()._2().get().getAuthors();
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//// List<Author> to_enrich_authors = r.getAuthor();
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//
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// return to_enrich_authors
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// .stream()
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// .map(a -> {
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// if (filter) {
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// if (containsAllowedPid(a)) {
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// return a;
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// }
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// }
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//
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// List<Author> lst = autoritative_authors.stream()
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// .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
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// if (lst.size() == 0) {
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// return a;
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// }
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// return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
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//
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// }).collect(Collectors.toList());
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// }
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//
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// private static void writeResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult,
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// String outputPath, String type) {
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//
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// results.join(toupdateresult)
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// .map(p -> {
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// Result r = p._2()._1();
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//
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// List<Author> autoritative_authors = p._2()._2().getAuthors();
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// List<eu.dnetlib.dhp.schema.oaf.Author> to_enrich_authors = r.getAuthor();
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//
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// r.setAuthor(enrichAutors(autoritative_authors, to_enrich_authors, false));
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//// .stream()
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//// .map(a -> {
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//// if(filter) {
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//// if (containsAllowedPid(a)) {
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//// return a;
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//// }
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//// }
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////
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//// List<Author> lst = autoritative_authors.stream()
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//// .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
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//// if(lst.size() == 0){
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//// return a;
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//// }
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//// return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
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////
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//// }).collect(Collectors.toList()));
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//
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// return r;
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// })
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// .map(p -> new ObjectMapper().writeValueAsString(p))
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// .saveAsTextFile(outputPath + "/" + type + "_update");
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// }
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// private static void updateResult(JavaPairRDD<String, Result> results, JavaPairRDD<String, TypedRow> toupdateresult,
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// String outputPath, String type) {
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// results.leftOuterJoin(toupdateresult)
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// .map(p -> {
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// Result r = p._2()._1();
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// if (p._2()._2().isPresent()){
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// List<AutoritativeAuthor> autoritative_authors = p._2()._2().get().getAuthors();
|
||
|
|
// List<eu.dnetlib.dhp.schema.oaf.Author> to_enrich_authors = r.getAuthor();
|
||
|
|
//
|
||
|
|
// r.setAuthor(enrichAutors(autoritative_authors, to_enrich_authors, true));
|
||
|
|
//// .stream()
|
||
|
|
//// .map(a -> {
|
||
|
|
//// if(filter) {
|
||
|
|
//// if (containsAllowedPid(a)) {
|
||
|
|
//// return a;
|
||
|
|
//// }
|
||
|
|
//// }
|
||
|
|
////
|
||
|
|
//// List<Author> lst = autoritative_authors.stream()
|
||
|
|
//// .map(aa -> enrichAuthor(aa, a)).filter(au -> !(au == null)).collect(Collectors.toList());
|
||
|
|
//// if(lst.size() == 0){
|
||
|
|
//// return a;
|
||
|
|
//// }
|
||
|
|
//// return lst.get(0);//Each author can be enriched at most once. It cannot be the same as many different people
|
||
|
|
////
|
||
|
|
//// }).collect(Collectors.toList()));
|
||
|
|
// }
|
||
|
|
// return r;
|
||
|
|
// })
|
||
|
|
// .map(p -> new ObjectMapper().writeValueAsString(p))
|
||
|
|
// .saveAsTextFile(outputPath+"/"+type);
|
||
|
|
// }
|
||
|
|
|
||
|
|
|
||
|
|
|
||
|
|
private static boolean containsAllowedPid(eu.dnetlib.dhp.schema.oaf.Author a) {
|
||
|
|
for (StructuredProperty pid : a.getPid()) {
|
||
|
|
if (PROPAGATION_AUTHOR_PID.equals(pid.getQualifier().getClassid())) {
|
||
|
|
return true;
|
||
|
|
}
|
||
|
|
}
|
||
|
|
return false;
|
||
|
|
}
|
||
|
|
|
||
|
|
}
|
||
|
|
|
||
|
|
|
||
|
|
/*private ResultProtos.Result.Metadata.Builder searchMatch(List<FieldTypeProtos.Author> author_list){
|
||
|
|
ResultProtos.Result.Metadata.Builder metadataBuilder = ResultProtos.Result.Metadata.newBuilder();
|
||
|
|
boolean updated = false;
|
||
|
|
|
||
|
|
for (FieldTypeProtos.Author a: author_list){
|
||
|
|
FieldTypeProtos.Author.Builder author = searchAuthor(a, autoritative_authors);
|
||
|
|
if(author != null){
|
||
|
|
updated = true;
|
||
|
|
metadataBuilder.addAuthor(author);
|
||
|
|
}else{
|
||
|
|
metadataBuilder.addAuthor(FieldTypeProtos.Author.newBuilder(a));
|
||
|
|
}
|
||
|
|
}
|
||
|
|
if(updated)
|
||
|
|
return metadataBuilder;
|
||
|
|
return null;
|
||
|
|
}
|
||
|
|
private FieldTypeProtos.Author.Builder searchAuthor(FieldTypeProtos.Author a, List<FieldTypeProtos.Author> author_list){
|
||
|
|
if(containsOrcid(a.getPidList()))
|
||
|
|
return null;
|
||
|
|
for(FieldTypeProtos.Author autoritative_author : author_list) {
|
||
|
|
if (equals(autoritative_author, a)) {
|
||
|
|
if(!containsOrcid(a.getPidList()))
|
||
|
|
return update(a, autoritative_author);
|
||
|
|
}
|
||
|
|
}
|
||
|
|
return null;
|
||
|
|
|
||
|
|
}
|
||
|
|
|
||
|
|
private boolean containsOrcid(List<FieldTypeProtos.KeyValue> pidList){
|
||
|
|
if(pidList == null)
|
||
|
|
return false;
|
||
|
|
return pidList
|
||
|
|
.stream()
|
||
|
|
.filter(kv -> kv.getKey().equals(PropagationConstants.AUTHOR_PID))
|
||
|
|
.collect(Collectors.toList()).size() > 0;
|
||
|
|
}
|
||
|
|
*/
|