[Person]First implementation to include Person entity in the graph
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package eu.dnetlib.dhp.actionmanager.personentity;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import java.io.Serializable;
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import java.util.ArrayList;
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public class Coauthors implements Serializable {
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private ArrayList<Relation> coauthors;
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public ArrayList<Relation> getCoauthors() {
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return coauthors;
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}
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public void setCoauthors(ArrayList<Relation> coauthors) {
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this.coauthors = coauthors;
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}
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}
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package eu.dnetlib.dhp.actionmanager.personentity;
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import eu.dnetlib.dhp.schema.oaf.Person;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import scala.Tuple2;
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import java.io.Serializable;
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public class Couples implements Serializable {
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Person p ;
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Relation r;
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public Couples() {
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}
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public Person getP() {
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return p;
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}
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public void setP(Person p) {
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this.p = p;
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}
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public Relation getR() {
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return r;
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}
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public void setR(Relation r) {
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this.r = r;
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}
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public static <Tuples> Couples newInstance(Tuple2<Person, Relation> couple){
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Couples c = new Couples();
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c.p = couple._1();
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c.r = couple._2();
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return c;
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}
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}
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package eu.dnetlib.dhp.actionmanager.personentity;
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import com.fasterxml.jackson.databind.ObjectMapper;
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import eu.dnetlib.dhp.actionmanager.Constants;
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import eu.dnetlib.dhp.application.ArgumentApplicationParser;
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import eu.dnetlib.dhp.collection.orcid.model.Author;
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import eu.dnetlib.dhp.collection.orcid.model.Employment;
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import eu.dnetlib.dhp.collection.orcid.model.Work;
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import eu.dnetlib.dhp.schema.action.AtomicAction;
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import eu.dnetlib.dhp.schema.common.ModelConstants;
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import eu.dnetlib.dhp.schema.common.ModelSupport;
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import eu.dnetlib.dhp.schema.oaf.KeyValue;
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import eu.dnetlib.dhp.schema.oaf.Person;
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import eu.dnetlib.dhp.schema.oaf.Relation;
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import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
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import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
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import eu.dnetlib.dhp.schema.oaf.Pid;
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import eu.dnetlib.dhp.schema.oaf.utils.PidCleaner;
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import eu.dnetlib.dhp.schema.oaf.utils.PidType;
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import eu.dnetlib.dhp.utils.DHPUtils;
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import org.apache.commons.cli.ParseException;
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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.hadoop.mapred.SequenceFileOutputFormat;
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import org.apache.spark.SparkConf;
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import org.apache.spark.api.java.function.*;
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import org.apache.spark.sql.*;
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import org.jetbrains.annotations.NotNull;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.spark_project.jetty.util.StringUtil;
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import scala.Tuple2;
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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.io.Serializable;
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import java.util.*;
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import java.util.stream.Collectors;
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import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession;
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public class ExtractPerson implements Serializable {
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private static final Logger log = LoggerFactory.getLogger(ExtractPerson.class);
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private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
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private static final String OPENAIRE_PREFIX = "openaire____";
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private static final String SEPARATOR = "::";
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private static final String orcidKey = "10|" + OPENAIRE_PREFIX + SEPARATOR + DHPUtils.md5(ModelConstants.ORCID.toLowerCase());
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private static final String DOI_PREFIX = "50|doi_________::";
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private static final String PMID_PREFIX = "50|pmid________::";
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private static final String ARXIV_PREFIX = "50|arXiv_______::";
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private static final String PMCID_PREFIX = "50|pmcid_______::";
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private static final String ROR_PREFIX = "20|ror_________::";
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private static final String PERSON_PREFIX = ModelSupport.getIdPrefix(Person.class) + "|orcid_______";
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public static final String ORCID_AUTHORS_CLASSID = "sysimport:crosswalk:orcid";
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public static final String ORCID_AUTHORS_CLASSNAME = "Imported from ORCID";
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public static void main(final String[] args) throws IOException, ParseException {
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final ArgumentApplicationParser parser = new ArgumentApplicationParser(
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IOUtils
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.toString(
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Objects
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.requireNonNull(
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ExtractPerson.class
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.getResourceAsStream(
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"/eu/dnetlib/dhp/actionmanager/personentity/as_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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log.info("isSparkSessionManaged: {}", isSparkSessionManaged);
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final String inputPath = parser.get("inputPath");
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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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final String workingDir = parser.get("workingDir");
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log.info("workingDir {}", workingDir);
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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 -> createActionSet(spark, inputPath, outputPath, workingDir));
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}
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private static void createActionSet(SparkSession spark, String inputPath, String outputPath, String workingDir) {
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Dataset<Author> authors = spark
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.read()
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.parquet(inputPath + "Authors").as(Encoders.bean(Author.class));
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Dataset<Work> works = spark
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.read()
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.parquet(inputPath + "Works")
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.as(Encoders.bean(Work.class))
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.filter((FilterFunction<Work>) w -> Optional.ofNullable(w.getPids()).isPresent() &&
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w.getPids().stream().anyMatch(p->p.getSchema().equalsIgnoreCase("doi") ||
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p.getSchema().equalsIgnoreCase("pmc") ||
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p.getSchema().equalsIgnoreCase("pmid") ||
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p.getSchema().equalsIgnoreCase("arxiv")));
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Dataset<Employment> employmentDataset = spark
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.read()
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.parquet(inputPath + "Employments")
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.as(Encoders.bean(Employment.class));
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Dataset<Author> peopleToMap = authors.joinWith(works, authors.col("orcid").equalTo(works.col("orcid")))
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.map((MapFunction<Tuple2<Author, Work>, Author>) t2 -> t2._1(), Encoders.bean(Author.class))
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.groupByKey((MapFunction<Author, String>) a -> a.getOrcid(), Encoders.STRING())
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.mapGroups((MapGroupsFunction<String, Author, Author>) (k, it) -> it.next(), Encoders.bean(Author.class));
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Dataset<Employment> employment = employmentDataset.joinWith(peopleToMap, employmentDataset.col("orcid").equalTo(peopleToMap.col("orcid")))
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.map((MapFunction<Tuple2<Employment, Author>, Employment>) t2 -> t2._1(), Encoders.bean(Employment.class));
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peopleToMap.show(false);
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Dataset<Person> people;
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people = peopleToMap.map((MapFunction<Author, Person>) op -> {
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Person person = new Person();
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person.setId(DHPUtils.generateIdentifier(op.getOrcid(), PERSON_PREFIX));
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person.setBiography(Optional.ofNullable(op.getBiography())
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.orElse(""));
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KeyValue kv = OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS);
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kv.setDataInfo(null);
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person.setCollectedfrom(Arrays.asList(kv));
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person.setAlternativeNames(Optional.ofNullable(op.getOtherNames())
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.orElse(new ArrayList<>()));
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person.setFamilyName(Optional.ofNullable(op.getFamilyName())
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.orElse(""));
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person.setGivenName(Optional.ofNullable(op.getGivenName())
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.orElse(""));
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person.setPid(Optional.ofNullable(op.getOtherPids())
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.map(v -> v.stream().map(p -> Pid.newInstance(p.getSchema(), p.getValue())).collect(Collectors.toList()))
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.orElse(new ArrayList<>())
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);
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person.getPid().add(Pid.newInstance(ModelConstants.ORCID, op.getOrcid()));
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person.setDateofcollection(op.getLastModifiedDate());
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person.setOriginalId(Arrays.asList(op.getOrcid()));
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return person;
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}, Encoders.bean(Person.class));
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people.show(false);
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Dataset<Relation> authorship;
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authorship = works
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.flatMap((FlatMapFunction<Work, Relation>) ExtractPerson::getAuthorshipRelationIterator
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, Encoders.bean(Relation.class));
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authorship.show(false);
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Dataset<Relation> coauthorship = works
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.flatMap((FlatMapFunction<Work, Tuple2<String, String>>) w -> {
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List<Tuple2<String, String>> lista = new ArrayList<>();
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w.getPids().stream().forEach(p -> {
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if (p.getSchema().equalsIgnoreCase("doi") || p.getSchema().equalsIgnoreCase("pmc") || p.getSchema().equalsIgnoreCase("pmid") || p.getSchema().equalsIgnoreCase("arxiv"))
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lista.add(new Tuple2<>(p.getValue(), w.getOrcid()));
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});
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return lista.iterator();
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}, Encoders.tuple(Encoders.STRING(), Encoders.STRING()))
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.groupByKey((MapFunction<Tuple2<String, String>, String>) Tuple2::_1, Encoders.STRING())
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.mapGroups((MapGroupsFunction<String, Tuple2<String, String>, Coauthors>) (k, it) ->
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extractCoAuthors(it), Encoders.bean(Coauthors.class))
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.flatMap((FlatMapFunction<Coauthors, Relation>) c -> c.getCoauthors().iterator(), Encoders.bean(Relation.class))
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.groupByKey((MapFunction<Relation, String>) r -> r.getSource() + r.getTarget(), Encoders.STRING())
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.mapGroups((MapGroupsFunction<String, Relation, Relation>) (k, it) -> it.next(), Encoders.bean(Relation.class));
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coauthorship.show(false);
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Dataset<Relation> affiliation = employment
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.filter((FilterFunction<Employment>) e -> Optional.ofNullable(e.getAffiliationId()).isPresent())
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.filter((FilterFunction<Employment>) e -> e.getAffiliationId().getSchema().equalsIgnoreCase("ror"))
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.map((MapFunction<Employment, Relation>) ExtractPerson::getAffiliationRelation
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, Encoders.bean(Relation.class));
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affiliation.show(false);
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people.toJavaRDD()
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.map(p -> new AtomicAction(p.getClass(), p))
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.union(authorship.toJavaRDD().map(r-> new AtomicAction(r.getClass(),r)))
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.union(coauthorship.toJavaRDD().map(r-> new AtomicAction(r.getClass(),r)))
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.union(affiliation.toJavaRDD().map(r->new AtomicAction(r.getClass(),r)))
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.mapToPair(
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aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()),
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new Text(OBJECT_MAPPER.writeValueAsString(aa))))
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.saveAsHadoopFile(
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outputPath, Text.class, Text.class, SequenceFileOutputFormat.class);//, GzipCodec.class);
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}
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private static Coauthors extractCoAuthors(Iterator<Tuple2<String, String>> it) {
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Coauthors coauth = new Coauthors();
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ArrayList<Relation> ret = new ArrayList<>();
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List<String> coauthors = new ArrayList<>();
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while(it.hasNext())
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coauthors.add(it.next()._2());
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for (int i = 0; i < coauthors.size() -1; i++ )
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for(int j = i + 1; j < coauthors.size(); j++)
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ret.addAll(getCoAuthorshipRelations(coauthors.get(i), coauthors.get(j)));
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coauth.setCoauthors(ret);
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return coauth;
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}
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private static Relation getAffiliationRelation(Employment row) {
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String source = PERSON_PREFIX + IdentifierFactory.md5(row.getOrcid());
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String target = ROR_PREFIX
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+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAffiliationId().getValue()));
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List<KeyValue> properties = new ArrayList<>() ;
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Relation relation =
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OafMapperUtils.getRelation(source, target, ModelConstants.ORG_PERSON_RELTYPE, ModelConstants.ORG_PERSON_SUBRELTYPE, ModelConstants.ORG_PERSON_PARTICIPATES ,
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Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
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OafMapperUtils.dataInfo(false, null, false, false,
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OafMapperUtils.qualifier(ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "0.91"),
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null);
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if(Optional.ofNullable(row.getStartDate()).isPresent() && StringUtil.isNotBlank(row.getStartDate())){
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KeyValue kv = new KeyValue();
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kv.setKey("startDate");
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kv.setValue(row.getStartDate());
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properties.add(kv);
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}
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if (Optional.ofNullable(row.getEndDate()).isPresent() && StringUtil.isNotBlank(row.getEndDate())) {
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KeyValue kv = new KeyValue();
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kv.setKey("endDate");
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kv.setValue(row.getEndDate());
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properties.add(kv);
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}
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if (properties.size() > 0)
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relation.setProperties(properties);
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return relation;
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}
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private static Collection<? extends Relation> getCoAuthorshipRelations(String orcid1, String orcid2) {
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String source = PERSON_PREFIX + IdentifierFactory.md5(orcid1);
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String target = PERSON_PREFIX + IdentifierFactory.md5(orcid2);
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return Arrays.asList(OafMapperUtils.getRelation(source, target,ModelConstants.PERSON_PERSON_RELTYPE,
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ModelConstants.PERSON_PERSON_SUBRELTYPE,
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ModelConstants.PERSON_PERSON_HASCOAUTHORED,
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Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
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OafMapperUtils.dataInfo(false, null, false, false,
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OafMapperUtils.qualifier(ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "0.91"),
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null),
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OafMapperUtils.getRelation(target, source,ModelConstants.PERSON_PERSON_RELTYPE,
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ModelConstants.PERSON_PERSON_SUBRELTYPE,
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ModelConstants.PERSON_PERSON_HASCOAUTHORED,
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Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
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OafMapperUtils.dataInfo(false, null, false, false,
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OafMapperUtils.qualifier(ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "0.91"),
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null));
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}
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private static @NotNull Iterator<Relation> getAuthorshipRelationIterator(Work w) {
|
||||||
|
|
||||||
|
if(Optional.ofNullable(w.getPids()).isPresent())
|
||||||
|
return w.getPids()
|
||||||
|
.stream()
|
||||||
|
.map(pid -> getRelation(w.getOrcid(), pid))
|
||||||
|
.filter(Objects::nonNull).collect(Collectors.toList()).iterator();
|
||||||
|
List<Relation> ret = new ArrayList<>();
|
||||||
|
return ret.iterator();
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
private static Relation getRelation(String orcid, eu.dnetlib.dhp.collection.orcid.model.Pid pid){
|
||||||
|
String target ;
|
||||||
|
String source = PERSON_PREFIX + "::" + IdentifierFactory.md5(orcid);
|
||||||
|
switch (pid.getSchema()){
|
||||||
|
case "doi":
|
||||||
|
target = DOI_PREFIX
|
||||||
|
+ IdentifierFactory
|
||||||
|
.md5(PidCleaner.normalizePidValue(PidType.doi.toString(), pid.getValue()));
|
||||||
|
break;
|
||||||
|
case "pmid":
|
||||||
|
target = PMID_PREFIX
|
||||||
|
+ IdentifierFactory
|
||||||
|
.md5(PidCleaner.normalizePidValue(PidType.pmid.toString(), pid.getValue()));
|
||||||
|
break;
|
||||||
|
case "arxiv":
|
||||||
|
target = ARXIV_PREFIX
|
||||||
|
+ IdentifierFactory
|
||||||
|
.md5(PidCleaner.normalizePidValue(PidType.arXiv.toString(), pid.getValue()));
|
||||||
|
break;
|
||||||
|
case "pmcid":
|
||||||
|
target = PMCID_PREFIX
|
||||||
|
+ IdentifierFactory
|
||||||
|
.md5(PidCleaner.normalizePidValue(PidType.pmc.toString(), pid.getValue()));
|
||||||
|
break;
|
||||||
|
|
||||||
|
default:
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
return OafMapperUtils.getRelation(source, target,ModelConstants.RESULT_PERSON_RELTYPE,
|
||||||
|
ModelConstants.RESULT_PERSON_SUBRELTYPE,
|
||||||
|
ModelConstants.RESULT_PERSON_HASAUTHORED,
|
||||||
|
Arrays.asList(OafMapperUtils.keyValue(orcidKey, ModelConstants.ORCID_DS)),
|
||||||
|
OafMapperUtils.dataInfo(false, null, false, false,
|
||||||
|
OafMapperUtils.qualifier(ORCID_AUTHORS_CLASSID, ORCID_AUTHORS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), "0.91"),
|
||||||
|
null);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,23 @@
|
||||||
|
package eu.dnetlib.dhp.actionmanager.personentity;
|
||||||
|
|
||||||
|
import eu.dnetlib.dhp.collection.orcid.model.Work;
|
||||||
|
import org.apache.hadoop.yarn.webapp.hamlet.Hamlet;
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
import java.util.ArrayList;
|
||||||
|
|
||||||
|
public class WorkList implements Serializable {
|
||||||
|
private ArrayList<Work> workArrayList;
|
||||||
|
|
||||||
|
public ArrayList<Work> getWorkArrayList() {
|
||||||
|
return workArrayList;
|
||||||
|
}
|
||||||
|
|
||||||
|
public void setWorkArrayList(ArrayList<Work> workArrayList) {
|
||||||
|
this.workArrayList = workArrayList;
|
||||||
|
}
|
||||||
|
|
||||||
|
public WorkList() {
|
||||||
|
workArrayList = new ArrayList<>();
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -104,8 +104,8 @@ public class CreateActionSetFromWebEntries implements Serializable {
|
||||||
final String ror = ROR_PREFIX
|
final String ror = ROR_PREFIX
|
||||||
+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
|
+ IdentifierFactory.md5(PidCleaner.normalizePidValue("ROR", row.getAs("ror")));
|
||||||
ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
|
ret.addAll(createAffiliationRelationPairDOI(row.getAs("doi"), ror));
|
||||||
ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
|
// ret.addAll(createAffiliationRelationPairPMID(row.getAs("pmid"), ror));
|
||||||
ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
|
// ret.addAll(createAffiliationRelationPairPMCID(row.getAs("pmcid"), ror));
|
||||||
|
|
||||||
return ret
|
return ret
|
||||||
.iterator();
|
.iterator();
|
||||||
|
|
@ -139,11 +139,17 @@ public class CreateActionSetFromWebEntries implements Serializable {
|
||||||
"institution", functions
|
"institution", functions
|
||||||
.explode(
|
.explode(
|
||||||
functions.col("institutions")))
|
functions.col("institutions")))
|
||||||
|
|
||||||
.selectExpr(
|
.selectExpr(
|
||||||
"id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror",
|
"id", "doi", "institution.ror as ror",
|
||||||
"institution.country_code as country_code", "publication_year")
|
"institution.country_code as country_code", "publication_year")
|
||||||
.distinct();
|
.distinct();
|
||||||
|
|
||||||
|
// .selectExpr(
|
||||||
|
// "id", "doi", "ids.pmcid as pmcid", "ids.pmid as pmid", "institution.ror as ror",
|
||||||
|
// "institution.country_code as country_code", "publication_year")
|
||||||
|
// .distinct();
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
private static Dataset<Row> readBlackList(SparkSession spark, String inputPath) {
|
private static Dataset<Row> readBlackList(SparkSession spark, String inputPath) {
|
||||||
|
|
|
||||||
|
|
@ -20,6 +20,9 @@ public class Author extends ORCIDItem {
|
||||||
|
|
||||||
private String lastModifiedDate;
|
private String lastModifiedDate;
|
||||||
|
|
||||||
|
public Author() {
|
||||||
|
}
|
||||||
|
|
||||||
public String getBiography() {
|
public String getBiography() {
|
||||||
return biography;
|
return biography;
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -11,4 +11,7 @@ public class ORCIDItem {
|
||||||
public void setOrcid(String orcid) {
|
public void setOrcid(String orcid) {
|
||||||
this.orcid = orcid;
|
this.orcid = orcid;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
public ORCIDItem() {
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -32,4 +32,6 @@ public class Work extends ORCIDItem {
|
||||||
pids.add(pid);
|
pids.add(pid);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
public Work() {
|
||||||
|
}
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,26 @@
|
||||||
|
[
|
||||||
|
{
|
||||||
|
"paramName": "ip",
|
||||||
|
"paramLongName": "inputPath",
|
||||||
|
"paramDescription": "the zipped opencitations file",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "op",
|
||||||
|
"paramLongName": "outputPath",
|
||||||
|
"paramDescription": "the working path",
|
||||||
|
"paramRequired": true
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "issm",
|
||||||
|
"paramLongName": "isSparkSessionManaged",
|
||||||
|
"paramDescription": "the hdfs name node",
|
||||||
|
"paramRequired": false
|
||||||
|
},
|
||||||
|
{
|
||||||
|
"paramName": "wd",
|
||||||
|
"paramLongName": "workingDir",
|
||||||
|
"paramDescription": "the hdfs name node",
|
||||||
|
"paramRequired": false
|
||||||
|
}
|
||||||
|
]
|
||||||
|
|
@ -0,0 +1,114 @@
|
||||||
|
|
||||||
|
package eu.dnetlib.dhp.actionmanager.person;
|
||||||
|
|
||||||
|
import com.fasterxml.jackson.databind.ObjectMapper;
|
||||||
|
import eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob;
|
||||||
|
import eu.dnetlib.dhp.actionmanager.personentity.ExtractPerson;
|
||||||
|
import eu.dnetlib.dhp.collection.orcid.model.Author;
|
||||||
|
import eu.dnetlib.dhp.schema.action.AtomicAction;
|
||||||
|
import eu.dnetlib.dhp.schema.common.ModelConstants;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.Relation;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions;
|
||||||
|
import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory;
|
||||||
|
import org.apache.commons.io.FileUtils;
|
||||||
|
import org.apache.hadoop.io.Text;
|
||||||
|
import org.apache.spark.SparkConf;
|
||||||
|
import org.apache.spark.api.java.JavaRDD;
|
||||||
|
import org.apache.spark.api.java.JavaSparkContext;
|
||||||
|
import org.apache.spark.api.java.function.FilterFunction;
|
||||||
|
import org.apache.spark.sql.Dataset;
|
||||||
|
import org.apache.spark.sql.Encoders;
|
||||||
|
import org.apache.spark.sql.SaveMode;
|
||||||
|
import org.apache.spark.sql.SparkSession;
|
||||||
|
import org.junit.jupiter.api.AfterAll;
|
||||||
|
import org.junit.jupiter.api.Assertions;
|
||||||
|
import org.junit.jupiter.api.BeforeAll;
|
||||||
|
import org.junit.jupiter.api.Test;
|
||||||
|
import org.slf4j.Logger;
|
||||||
|
import org.slf4j.LoggerFactory;
|
||||||
|
|
||||||
|
import java.io.IOException;
|
||||||
|
import java.nio.file.Files;
|
||||||
|
import java.nio.file.Path;
|
||||||
|
import java.util.Optional;
|
||||||
|
|
||||||
|
import static org.junit.jupiter.api.Assertions.assertEquals;
|
||||||
|
|
||||||
|
public class CreatePersonAS {
|
||||||
|
|
||||||
|
private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper();
|
||||||
|
|
||||||
|
private static SparkSession spark;
|
||||||
|
|
||||||
|
private static Path workingDir;
|
||||||
|
private static final Logger log = LoggerFactory
|
||||||
|
.getLogger(CreatePersonAS.class);
|
||||||
|
|
||||||
|
@BeforeAll
|
||||||
|
public static void beforeAll() throws IOException {
|
||||||
|
workingDir = Files
|
||||||
|
.createTempDirectory(CreatePersonAS.class.getSimpleName());
|
||||||
|
log.info("using work dir {}", workingDir);
|
||||||
|
|
||||||
|
SparkConf conf = new SparkConf();
|
||||||
|
conf.setAppName(CreatePersonAS.class.getSimpleName());
|
||||||
|
|
||||||
|
conf.setMaster("local[*]");
|
||||||
|
conf.set("spark.driver.host", "localhost");
|
||||||
|
conf.set("hive.metastore.local", "true");
|
||||||
|
conf.set("spark.ui.enabled", "false");
|
||||||
|
conf.set("spark.sql.codegen.wholeStage","false");
|
||||||
|
conf.set("spark.sql.warehouse.dir", workingDir.toString());
|
||||||
|
conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString());
|
||||||
|
|
||||||
|
spark = SparkSession
|
||||||
|
.builder()
|
||||||
|
.appName(CreatePersonAS.class.getSimpleName())
|
||||||
|
.config(conf)
|
||||||
|
.getOrCreate();
|
||||||
|
}
|
||||||
|
|
||||||
|
@AfterAll
|
||||||
|
public static void afterAll() throws IOException {
|
||||||
|
FileUtils.deleteDirectory(workingDir.toFile());
|
||||||
|
spark.stop();
|
||||||
|
}
|
||||||
|
|
||||||
|
@Test
|
||||||
|
void testAuthors() throws Exception {
|
||||||
|
|
||||||
|
String inputPath = getClass()
|
||||||
|
.getResource(
|
||||||
|
"/eu/dnetlib/dhp/actionmanager/person/")
|
||||||
|
.getPath();
|
||||||
|
|
||||||
|
// spark
|
||||||
|
// .read()
|
||||||
|
// .parquet(inputPath + "Authors")
|
||||||
|
// .as(Encoders.bean(Author.class))
|
||||||
|
// .filter((FilterFunction<Author>) a -> Optional.ofNullable(a.getOtherNames()).isPresent() &&
|
||||||
|
// Optional.ofNullable(a.getBiography()).isPresent())
|
||||||
|
// .write()
|
||||||
|
// .mode(SaveMode.Overwrite)
|
||||||
|
// .parquet(workingDir.toString() + "AuthorsSubset");
|
||||||
|
|
||||||
|
|
||||||
|
ExtractPerson
|
||||||
|
.main(
|
||||||
|
new String[] {
|
||||||
|
"-isSparkSessionManaged",
|
||||||
|
Boolean.FALSE.toString(),
|
||||||
|
"-inputPath",
|
||||||
|
inputPath,
|
||||||
|
"-outputPath",
|
||||||
|
workingDir.toString() + "/actionSet1",
|
||||||
|
"-workingDir",
|
||||||
|
workingDir.toString() + "/working"
|
||||||
|
});
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -0,0 +1,10 @@
|
||||||
|
{"orcid":"0000-0001-6291-9619","title":"A Visible Light Driven Photoelectrochemical Chloramphenicol Aptasensor Based on a Gold Nanoparticle-Functionalized 3D Flower-like MoS<sub>2</sub>/TiO<sub>2</sub> Heterostructure","pids":[{"value":"10.1021/acs.langmuir.1c02956","schema":"doi"},{"value":"2-s2.0-85124885368","schema":"eid"},{"value":"15205827 07437463","schema":"issn"}]}
|
||||||
|
{"orcid":"0000-0002-3210-3034","title":"A Visible Light Driven Photoelectrochemical Chloramphenicol Aptasensor Based on a Gold Nanoparticle-Functionalized 3D Flower-like MoS<sub>2</sub>/TiO<sub>2</sub> Heterostructure","pids":[{"value":"10.1021/acs.langmuir.1c02956","schema":"doi"},{"value":"2-s2.0-85124885368","schema":"eid"},{"value":"15205827 07437463","schema":"issn"}]}
|
||||||
|
{"orcid":"0000-0001-6291-9619","title":"Study of High-Transverse-Momentum Higgs Boson Production in Association with a Vector Boson in the <math display=\"inline\"><mrow><mi>q</mi><mi>q</mi><mi>b</mi><mi>b</mi></mrow></math> Final State with the ATLAS Detector","pids":[{"value":"2736741","schema":"other-id"},{"value":"10.1103/PhysRevLett.132.131802","schema":"doi"},{"value":"2312.07605","schema":"arxiv"}]}
|
||||||
|
{"orcid":"0000-0002-3210-3034","title":"Study of High-Transverse-Momentum Higgs Boson Production in Association with a Vector Boson in the <math display=\"inline\"><mrow><mi>q</mi><mi>q</mi><mi>b</mi><mi>b</mi></mrow></math> Final State with the ATLAS Detector","pids":[{"value":"2736741","schema":"other-id"},{"value":"10.1103/PhysRevLett.132.131802","schema":"doi"},{"value":"2312.07605","schema":"arxiv"}]}
|
||||||
|
{"orcid":"0000-0002-9030-7609","title":"Search for supersymmetry in a final state containing two photons and missing transverse momentum in √s = 13 TeV pp collisions at the LHC using the ATLAS detector","pids":[{"value":"10.1140/epjc/s10052-016-4344-x","schema":"doi"},{"value":"2-s2.0-84988710988","schema":"eid"},{"value":"14346052 14346044","schema":"issn"}]}
|
||||||
|
{"orcid":"0000-0003-2552-9691","title":"Search for supersymmetry in a final state containing two photons and missing transverse momentum in $\\sqrt{s}$ = 13 TeV $pp$ collisions at the LHC using the ATLAS detector","pids":[{"value":"1473744","schema":"other-id"},{"value":"10.1140/epjc/s10052-016-4344-x","schema":"doi"},{"value":"1606.09150","schema":"arxiv"}]}
|
||||||
|
{"orcid":"0000-0003-0305-8980","title":"Search for supersymmetry in a final state containing two photons and missing transverse momentum in √s = 13 TeV pp collisions at the LHC using the ATLAS detector","pids":[{"value":"10.1140/epjc/s10052-016-4344-x","schema":"doi"},{"value":"2-s2.0-84988710988","schema":"eid"}]}
|
||||||
|
{"orcid":"0000-0002-9030-7609","title":"Measurement of the energy response of the ATLAS calorimeter to charged pions from $W^{\\pm }\\rightarrow \\tau ^{\\pm }(\\rightarrow \\pi ^{\\pm }\\nu _{\\tau })\\nu _{\\tau }$ events in Run 2 data","pids":[{"value":"1909507","schema":"other-id"},{"value":"10.1140/epjc/s10052-022-10117-2","schema":"doi"},{"value":"2108.09043","schema":"arxiv"}]}
|
||||||
|
{"orcid":"0000-0003-2629-4046","title":"Measurement of the energy response of the ATLAS calorimeter to charged pions from $W^{\\pm }\\rightarrow \\tau ^{\\pm }(\\rightarrow \\pi ^{\\pm }\\nu _{\\tau })\\nu _{\\tau }$ events in Run 2 data","pids":[{"value":"1909507","schema":"other-id"},{"value":"10.1140/epjc/s10052-022-10117-2","schema":"doi"},{"value":"2108.09043","schema":"arxiv"}]}
|
||||||
|
{"orcid":"0000-0001-8582-8912","title":"Measurement of the energy response of the ATLAS calorimeter to charged pions from $W^{\\pm }\\rightarrow \\tau ^{\\pm }(\\rightarrow \\pi ^{\\pm }\\nu _{\\tau })\\nu _{\\tau }$ events in Run 2 data","pids":[{"value":"1909507","schema":"other-id"},{"value":"10.1140/epjc/s10052-022-10117-2","schema":"doi"},{"value":"2108.09043","schema":"arxiv"}]}
|
||||||
19
pom.xml
19
pom.xml
|
|
@ -994,6 +994,25 @@
|
||||||
|
|
||||||
<!-- Build with scala 12 and Spark 3.4 -->
|
<!-- Build with scala 12 and Spark 3.4 -->
|
||||||
<profiles>
|
<profiles>
|
||||||
|
<!-- Activate ARM-compatible snappy dependency on new Silicon Macs -->
|
||||||
|
<profile>
|
||||||
|
<id>arm-silicon-mac</id>
|
||||||
|
<activation>
|
||||||
|
<os>
|
||||||
|
<arch>aarch64</arch>
|
||||||
|
<family>mac</family>
|
||||||
|
</os>
|
||||||
|
</activation>
|
||||||
|
<dependencyManagement>
|
||||||
|
<dependencies>
|
||||||
|
<dependency>
|
||||||
|
<groupId>org.xerial.snappy</groupId>
|
||||||
|
<artifactId>snappy-java</artifactId>
|
||||||
|
<version>1.1.8.4</version>
|
||||||
|
</dependency>
|
||||||
|
</dependencies>
|
||||||
|
</dependencyManagement>
|
||||||
|
</profile>
|
||||||
<profile>
|
<profile>
|
||||||
<id>spark-34</id>
|
<id>spark-34</id>
|
||||||
<properties>
|
<properties>
|
||||||
|
|
|
||||||
Loading…
Reference in New Issue